annotate bowtie2_wrapper.xml @ 6:e23b0cdeeba6 draft

planemo upload commit 5ad726dc73203a704666033cd3bf70b82575978f
author devteam
date Wed, 26 Aug 2015 12:46:11 -0400
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1 <tool id="bowtie2" name="Bowtie2" version="0.6">
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2 <!-- Wrapper compatible with Bowtie version 2.2.4 -->
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3 <description>- map reads against reference genome</description>
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4 <macros>
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5 <import>read_group_macros.xml</import>
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6 </macros>
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7 <version_command>bowtie2 --version</version_command>
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8 <requirements>
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9 <requirement type="package" version="2.2.4">bowtie2</requirement>
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10 <requirement type="package" version="0.1.18">samtools</requirement>
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11 </requirements>
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12 <command>
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13
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14 ## prepare bowtie2 index
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15 #set index_path = ''
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16 #if str($reference_genome.source) == "history":
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17 bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
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18 ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
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19 #set index_path = 'genome'
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20 #else:
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21 #set index_path = $reference_genome.index.fields.path
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22 #end if
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23
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24 ## execute bowtie2
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25
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26 bowtie2
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27
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28 ## number of threads
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29 -p \${GALAXY_SLOTS:-4}
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30
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31 ## index file path
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32 -x $index_path
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33
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34
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35 ## Fastq inputs
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36 #if str( $library.type ) == "single":
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37 -U "${library.input_1}"
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38 #if str( $library.unaligned_file ) == "true":
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39 --un $output_unaligned_reads_l
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40 #end if
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41 #elif str( $library.type ) == "paired":
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42 -1 "${library.input_1}"
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43 -2 "${library.input_2}"
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44 #if str( $library.paired_options.paired_options_selector ) == "yes":
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45 -I "${library.paired_options.I}"
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46 -X "${library.paired_options.X}"
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47 ${library.paired_options.fr_rf_ff}
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48 ${library.paired_options.no_mixed}
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49 ${library.paired_options.no_discordant}
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50 ${library.paired_options.dovetail}
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51 ${library.paired_options.no_contain}
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52 ${library.paired_options.no_overlap}
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53 #end if
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54 #if str( $library.unaligned_file ) == "true":
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55 --un-conc $output_unaligned_reads_l
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56 #end if
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57 #else
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58 ## prepare collection
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59 -1 $library.input_1.forward
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60 -2 $library.input_1.reverse
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61 #if str( $library.paired_options.paired_options_selector ) == "yes":
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62 -I "${library.paired_options.I}"
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63 -X "${library.paired_options.X}"
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64 ${library.paired_options.fr_rf_ff}
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65 ${library.paired_options.no_mixed}
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66 ${library.paired_options.no_discordant}
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67 ${library.paired_options.dovetail}
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68 ${library.paired_options.no_contain}
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69 ${library.paired_options.no_overlap}
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70 #end if
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71 #if str( $library.unaligned_file ) == "true":
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72 --un-conc $output_unaligned_reads_l
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73 #end if
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74 #end if
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75
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76 ## Read group information.
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77 @define_read_group_helpers@
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78 #if str( $library.type ) == "single":
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79 #set $rg_auto_name = $read_group_name_default($library.input_1)
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80 #elif str( $library.type ) == "paired":
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81 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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82 #else
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83 #set $rg_auto_name = $read_group_name_default($library.input_1)
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84 #end if
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85 @set_use_rg_var@
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86 @set_read_group_vars@
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87 #if $use_rg
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88 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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89 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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90 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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91 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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92 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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93 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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94 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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95 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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96 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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97 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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98 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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99 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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100 #end if
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101
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102 ## Analysis type
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103 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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104 $analysis_type.presets
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105 #elif str( $analysis_type.analysis_type_selector ) == "full":
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106 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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107 --skip "${analysis_type.input_options.skip}"
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108 --qupto "${analysis_type.input_options.qupto}"
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109 --trim5 "${analysis_type.input_options.trim5}"
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110 --trim3 "${analysis_type.input_options.trim3}"
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111 ${analysis_type.input_options.qv_encoding}
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112 ${analysis_type.input_options.solexa_quals}
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113 ${analysis_type.input_options.int_quals}
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114 #end if
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115
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116 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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117 -N "${analysis_type.alignment_options.N}"
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118 -L "${analysis_type.alignment_options.L}"
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119 -i "${analysis_type.alignment_options.i}"
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120 --n-ceil "${analysis_type.alignment_options.n_ceil}"
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121 --dpad "${analysis_type.alignment_options.dpad}"
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122 --gbar "${analysis_type.alignment_options.gbar}"
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123 ${analysis_type.alignment_options.ignore_quals}
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124 ${analysis_type.alignment_options.nofw}
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125 ${analysis_type.alignment_options.norc}
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126 ${analysis_type.alignment_options.no_1mm_upfront}
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127 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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128 --end-to-end
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129 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
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130 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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131 --local
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132 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
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133 #end if
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134 #end if
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135
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136 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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137 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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138 --ma "${analysis_type.scoring_options.ma}"
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139 #end if
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140 --mp "${analysis_type.scoring_options.mp}"
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141 --np "${analysis_type.scoring_options.np}"
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142 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
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143 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
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144 #end if
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145
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146 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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147 -k "${analysis_type.reporting_options.k}"
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148 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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149 -a
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150 #end if
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151
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152 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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153 -D "${analysis_type.effort_options.D}"
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154 -R "${analysis_type.effort_options.R}"
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155 #end if
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156
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157 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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158 ${analysis_type.sam_options.no_unal}
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159 ${analysis_type.sam_options.omit_sec_seq}
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160 #end if
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161
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162 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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163 ${analysis_type.other_options.non_deterministic}
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164 --seed "${analysis_type.other_options.seed}"
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165 #end if
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166
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167 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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168 ${analysis_type.cline}
4
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169 #end if
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170
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171 -S "galaxy_bowtie_2_output.sam" &amp;&amp;
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172
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173 ## view/sort and output BAM file
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174 ( samtools view -Su "galaxy_bowtie_2_output.sam" | samtools sort -o - - > $output )
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175
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176 ## rename unaligned sequence files
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177 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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178 #from os.path import splitext
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179 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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180 &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
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181 &amp;&amp; mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }"
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182 #end if
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183
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184 </command>
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185
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186 <!-- basic error handling -->
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187 <stdio>
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188 <exit_code range="1:" level="fatal" description="Tool exception" />
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189 </stdio>
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190
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191 <inputs>
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192 <!-- single/paired -->
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193 <conditional name="library">
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194 <param name="type" type="select" label="Is this single or paired library">
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195 <option value="single">Single-end</option>
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196 <option value="paired">Paired-end</option>
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197 <option value="paired_collection">Paired-end Dataset Collection</option>
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198 </param>
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199
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200 <when value="single">
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201 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
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202 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
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203 </when>
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204 <when value="paired">
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205 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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206 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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207 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
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208 <conditional name="paired_options">
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209 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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210 <option value="no" selected="True">No</option>
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211 <option value="yes">Yes</option>
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212 </param>
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213 <when value="yes">
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214 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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215 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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216 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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217 <option value="--fr" selected="True">--fr</option>
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218 <option value="--rf">--rf</option>
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219 <option value="--ff">--ff</option>
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220 </param>
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221 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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222 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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223 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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224 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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225 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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226 </when>
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227 <when value="no">
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228 <!-- do nothing -->
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229 </when>
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230 </conditional>
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231 </when>
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232 <when value="paired_collection">
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233 <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
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234 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc; This triggers --un parameter for single reads and --un-conc for paired reads" />
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235 <conditional name="paired_options">
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236 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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237 <option value="no" selected="True">No</option>
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238 <option value="yes">Yes</option>
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239 </param>
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240 <when value="yes">
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241 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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242 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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243 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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244 <option value="--fr" selected="True">--fr</option>
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245 <option value="--rf">--rf</option>
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246 <option value="--ff">--ff</option>
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247 </param>
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248 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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249 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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250 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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251 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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252 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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253 </when>
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254 <when value="no">
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255 <!-- do nothing -->
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256 </when>
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257 </conditional>
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258 </when>
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259 </conditional>
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260
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261 <!-- reference genome -->
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262 <conditional name="reference_genome">
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263 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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264 <option value="indexed">Use a built-in genome index</option>
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265 <option value="history">Use a genome from the history and build index</option>
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266 </param>
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267 <when value="indexed">
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268 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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269 <options from_data_table="bowtie2_indexes">
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270 <filter type="sort_by" column="2"/>
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271 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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272 </options>
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273 </param>
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274 </when>
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275 <when value="history">
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276 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
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277 </when>
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278 </conditional>
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279
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280 <!-- read group settings -->
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281 <expand macro="read_group_conditional" />
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282 <conditional name="analysis_type">
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283 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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284 <option value="simple">1: Default setting only</option>
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285 <option value="full">2: Full parameter list</option>
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286 </param>
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287 <when value="simple">
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288 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
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289 <option value="no_presets" selected="True">No, just use defaults</option>
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290 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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291 <option value="--fast">Fast end-to-end (--fast)</option>
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292 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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293 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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294 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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295 <option value="--fast-local">Fast local (--fast-local)</option>
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296 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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297 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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298 </param>
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299 </when>
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300 <when value="full">
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301 <conditional name="input_options">
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302 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
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303 <option value="yes">Yes</option>
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304 <option value="no" selected="true">No</option>
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305 </param>
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306 <when value="yes">
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307 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
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308 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
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309 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
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310 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
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311 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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312 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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313 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
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314 </param>
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315 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
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316 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
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317 </when>
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318 <when value="no">
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319 <!-- do nothing -->
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320 </when>
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321 </conditional>
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322 <conditional name="alignment_options">
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323 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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324 <option value="yes">Yes</option>
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325 <option value="no" selected="true">No</option>
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326 </param>
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327 <when value="yes">
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328 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
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329 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
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330 <param name="i" type="text" value="S,1,1.15" size="10" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
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331 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
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332 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
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333 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
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334 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" selected="False" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
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335 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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336 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" selected="False" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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337 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" selected="False" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
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338 <conditional name="align_mode">
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339 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
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340 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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341 <option value="local">Local (--local)</option>
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342 </param>
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343 <when value="end-to-end">
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344 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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345 </when>
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346 <when value="local">
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347 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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348 </when>
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349 </conditional>
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350 </when>
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351 <when value="no">
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352 <!-- do nothing -->
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353 </when>
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354 </conditional>
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355 <conditional name="scoring_options">
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356 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
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357 <option value="yes">Yes</option>
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358 <option value="no" selected="true">No</option>
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359 </param>
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360 <when value="yes">
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361 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
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362 <param name="mp" type="text" size="10" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
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363 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
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364 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
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365 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
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366 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
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367 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
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368 </when>
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369 <when value="no">
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370 <!-- do nothing -->
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371 </when>
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372 </conditional>
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373 <conditional name="reporting_options">
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374 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
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375 <option value="no" selected="true">No, do not set</option>
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376 <option value="k">Set -k option and enter -k value</option>
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377 <option value="a">Set -a option</option>
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378 </param>
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379 <when value="no">
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380 <!-- do nothing -->
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381 </when>
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382 <when value="k">
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383 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
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384 </when>
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385 <when value="a">
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386 <!-- do nothing here; set -a flag on the command line-->
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387 </when>
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388 </conditional>
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389 <conditional name="effort_options">
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390 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
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391 <option value="yes">Yes</option>
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392 <option value="no" selected="true">No</option>
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393 </param>
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394 <when value="yes">
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395 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
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396 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
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397 </when>
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398 <when value="no">
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399 <!-- do nothing -->
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400 </when>
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401 </conditional>
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402
2
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403 <conditional name="sam_options">
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404 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
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405 <option value="yes">Yes</option>
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406 <option value="no" selected="true">No</option>
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407 </param>
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408 <when value="yes">
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409 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
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410 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
2
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411 </when>
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412 <when value="no">
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413 <!-- do nothing -->
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414 </when>
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415 </conditional>
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416 <conditional name="other_options">
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417 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
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418 <option value="yes">Yes</option>
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419 <option value="no" selected="true">No</option>
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420 </param>
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421 <when value="yes">
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422 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
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423 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
2
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424 </when>
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425 <when value="no">
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426 <!-- do nothing -->
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427 </when>
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428 </conditional>
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429 </when>
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430 </conditional>
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431 </inputs>
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432
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433 <!-- define outputs -->
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434
0
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435 <outputs>
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436
0
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437 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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438 <filter>library['unaligned_file'] is True</filter>
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439 <actions>
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440 <action type="format">
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441 <option type="from_param" name="library.input_1" param_attribute="ext" />
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442 </action>
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443 </actions>
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444 </data>
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445 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
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446 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
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447 <actions>
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448 <action type="format">
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449 <option type="from_param" name="library.input_1" param_attribute="ext" />
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450 </action>
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451 </actions>
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452 </data>
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453
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454 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
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455 <actions>
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456 <conditional name="reference_genome.source">
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457 <when value="indexed">
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458 <action type="metadata" name="dbkey">
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459 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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460 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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461 <filter type="param_value" ref="reference_genome.index" column="0"/>
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462 </option>
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463 </action>
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464 </when>
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465 <when value="history">
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466 <action type="metadata" name="dbkey">
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467 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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468 </action>
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469 </when>
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470 </conditional>
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471 </actions>
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472 </data>
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473
0
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474 </outputs>
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475
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476 <tests>
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477 <test>
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478 <!-- basic test on single paired default run -->
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479 <param name="type" value="paired"/>
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480 <param name="selection" value="no"/>
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481 <param name="paired_options_selector" value="no"/>
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482 <param name="unaligned_file" value="false"/>
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483 <param name="analysis_type_selector" value="simple"/>
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484 <param name="source" value="history" />
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485 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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486 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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487 <param name="own_file" value="bowtie2-ref.fasta" />
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488 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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489 </test>
5
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490 <test>
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491 <!-- basic test on single paired default run -->
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492 <param name="type" value="paired"/>
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493 <param name="selection" value="no"/>
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494 <param name="paired_options_selector" value="no"/>
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495 <param name="unaligned_file" value="false"/>
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496 <param name="analysis_type_selector" value="simple"/>
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497 <param name="rg_selector" value="set"/>
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498 <param name="ID" value="rg1"/>
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499 <param name="PL" value="CAPILLARY"/>
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500 <param name="source" value="history" />
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501 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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502 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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503 <param name="own_file" value="bowtie2-ref.fasta" />
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504 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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505 </test>
0
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506 </tests>
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507
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508 <help>
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509
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510 **Bowtie2 Overview**
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511
2
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512 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
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513 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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514
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515 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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516 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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517 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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518
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519 -----
0
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520
2
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521 **Selecting reference genomes for Bowtie2**
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522
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523 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
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524
2
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525 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.
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526 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.
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527
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528 If your genome of interest is not listed here you have two choices:
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529
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530 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
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531 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
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532
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533 ------
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534
2
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535 .. class:: infomark
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536
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537 **Bowtie2 options**
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538
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539 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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540
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541 -----
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542
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543 **Inputs**
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544
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545 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
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546
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547 ------
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548
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549 **Input options**::
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550
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551 -s/--skip &lt;int&gt;
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552 Skip (i.e. do not align) the first `&lt;int&gt;` reads or pairs in the input.
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553
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554 -u/--qupto &lt;int&gt;
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555 Align the first `&lt;int&gt;` reads or read pairs from the input (after the
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556 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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557
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558 -5/--trim5 &lt;int&gt;
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559 Trim `&lt;int&gt;` bases from 5' (left) end of each read before alignment (default: 0).
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560
2
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561 -3/--trim3 &lt;int&gt;
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562 Trim `&lt;int&gt;` bases from 3' (right) end of each read before alignment (default: 0).
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563
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564 --phred33
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565 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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566 also called the "Phred+33" encoding, which is used by the very latest Illumina
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567 pipelines.
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568
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569 --phred64
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570 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
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571 also called the "Phred+64" encoding.
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572
2
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573 --solexa-quals
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574 Convert input qualities from Solexa Phred quality (which can be negative) to
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575 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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576 Pipeline versions (prior to 1.3). Default: off.
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577
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578 --int-quals
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579 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
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580 Integers are treated as being on the Phred quality scale unless
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581 `--solexa-quals` is also specified. Default: off.
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582
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583 ------
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584
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585 **Presets in `--end-to-end` mode**::
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586
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587 --very-fast
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diff changeset
588 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
589
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parents: 0
diff changeset
590 --fast
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parents: 0
diff changeset
591 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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parents: 0
diff changeset
592
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593 --sensitive
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diff changeset
594 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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parents: 0
diff changeset
595
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596 --very-sensitive
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diff changeset
597 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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devteam
parents:
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598
96d2e31a3938 Imported from capsule None
devteam
parents:
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599 ------
96d2e31a3938 Imported from capsule None
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parents:
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600
2
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diff changeset
601 **Presets options in `--local` mode**::
0
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parents:
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602
2
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parents: 0
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603 --very-fast-local
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parents: 0
diff changeset
604 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
96d2e31a3938 Imported from capsule None
devteam
parents:
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605
2
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606 --fast-local
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parents: 0
diff changeset
607 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
96d2e31a3938 Imported from capsule None
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parents:
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608
2
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parents: 0
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609 --sensitive-local
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610 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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parents:
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611
2
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612 --very-sensitive-local
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parents: 0
diff changeset
613 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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parents: 0
diff changeset
614
0
96d2e31a3938 Imported from capsule None
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615 ------
96d2e31a3938 Imported from capsule None
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616
2
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diff changeset
617 **Alignment options**::
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618
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619 -N &lt;int&gt;
3
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parents: 2
diff changeset
620 Sets the number of mismatches to allowed in a seed alignment during multiseed
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parents: 2
diff changeset
621 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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parents: 0
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622 (often much slower) but increases sensitivity. Default: 0.
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623
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624 -L &lt;int&gt;
3
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parents: 2
diff changeset
625 Sets the length of the seed substrings to align during multiseed alignment.
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parents: 2
diff changeset
626 Smaller values make alignment slower but more sensitive. Default: the
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diff changeset
627 `--sensitive` preset is used by default, which sets `-L` to 22 in
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parents: 2
diff changeset
628 `--end-to-end` mode and to 20 in `--local` mode.
2
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parents: 0
diff changeset
629
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630 -i &lt;func&gt;
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parents: 0
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631 Sets a function governing the interval between seed substrings to use during
3
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632 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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633 length is 10, and the seed interval is 6, the seeds extracted will be:
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634
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parents: 0
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635 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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parents: 0
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636 Seed 1 fw: TAGCTACGCT
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parents: 0
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637 Seed 1 rc: AGCGTAGCTA
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638 Seed 2 fw: CGCTCTACGC
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639 Seed 2 rc: GCGTAGAGCG
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640 Seed 3 fw: ACGCTATCAT
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parents: 0
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641 Seed 3 rc: ATGATAGCGT
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parents: 0
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642 Seed 4 fw: TCATGCATAA
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parents: 0
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643 Seed 4 rc: TTATGCATGA
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parents: 0
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644
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parents: 0
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645 Since it's best to use longer intervals for longer reads, this parameter sets
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646 the interval as a function of the read length, rather than a single
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647 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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diff changeset
648 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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parents: 2
diff changeset
649 If the function returns a result less than
2
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parents: 0
diff changeset
650 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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diff changeset
651 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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652 in `--local` mode.
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653
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parents: 0
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654 --n-ceil &lt;func&gt;
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parents: 0
diff changeset
655 Sets a function governing the maximum number of ambiguous characters (usually
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diff changeset
656 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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657 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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diff changeset
658 where x is the read length. Reads exceeding this ceiling are filtered out.
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parents: 2
diff changeset
659 Default: `L,0,0.15`.
2
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parents: 0
diff changeset
660
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parents: 0
diff changeset
661 --dpad &lt;int&gt;
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parents: 0
diff changeset
662 "Pads" dynamic programming problems by `&lt;int&gt;` columns on either side to allow
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parents: 0
diff changeset
663 gaps. Default: 15.
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parents: 0
diff changeset
664
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parents: 0
diff changeset
665 --gbar &lt;int&gt;
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parents: 0
diff changeset
666 Disallow gaps within `&lt;int&gt;` positions of the beginning or end of the read.
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parents: 0
diff changeset
667 Default: 4.
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parents: 0
diff changeset
668
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parents: 0
diff changeset
669 --ignore-quals
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parents: 0
diff changeset
670 When calculating a mismatch penalty, always consider the quality value at the
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diff changeset
671 mismatched position to be the highest possible, regardless of the actual value.
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parents: 0
diff changeset
672 I.e. input is treated as though all quality values are high. This is also the
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diff changeset
673 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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parents: 0
diff changeset
674 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
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parents:
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675
2
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parents: 0
diff changeset
676 --nofw/--norc
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parents: 0
diff changeset
677 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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diff changeset
678 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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diff changeset
679 not attempt to align unpaired reads against the reverse-complement (Crick)
c1ec08cb34f9 Uploaded
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diff changeset
680 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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parents: 0
diff changeset
681 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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diff changeset
682 paired-end configurations corresponding to fragments from the reverse-complement
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diff changeset
683 (Crick) strand. Default: both strands enabled.
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diff changeset
684
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parents: 0
diff changeset
685 --no-1mm-upfront
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parents: 0
diff changeset
686 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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parents: 2
diff changeset
687 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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parents: 0
diff changeset
688 alignments can be found very quickly, and many short read alignments have exact or
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parents: 0
diff changeset
689 near-exact end-to-end alignments. However, this can lead to unexpected
3
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parents: 2
diff changeset
690 alignments when the user also sets options governing the multiseed heuristic,
2
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parents: 0
diff changeset
691 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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parents: 0
diff changeset
692 to the length of the read, the user will be surprised to find 1-mismatch alignments
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parents: 0
diff changeset
693 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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parents: 2
diff changeset
694 alignments before using the multiseed heuristic, which leads to the expected
2
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parents: 0
diff changeset
695 behavior when combined with options such as `-L` and `-N`. This comes at the
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diff changeset
696 expense of speed.
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diff changeset
697
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parents: 0
diff changeset
698 --end-to-end
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parents: 0
diff changeset
699 In this mode, Bowtie 2 requires that the entire read align from one end to the
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diff changeset
700 other, without any trimming (or "soft clipping") of characters from either end.
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parents: 0
diff changeset
701 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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parents: 0
diff changeset
702 are less than or equal to 0, and the greatest possible alignment score is 0.
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parents: 0
diff changeset
703 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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parents:
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704
2
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parents: 0
diff changeset
705 --local
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parents: 0
diff changeset
706 In this mode, Bowtie 2 does not require that the entire read align from one end
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devteam
parents: 0
diff changeset
707 to the other. Rather, some characters may be omitted ("soft clipped") from the
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parents: 0
diff changeset
708 ends in order to achieve the greatest possible alignment score. The match bonus
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parents: 0
diff changeset
709 `--ma` is used in this mode, and the best possible alignment score is equal to
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devteam
parents: 0
diff changeset
710 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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devteam
parents: 0
diff changeset
711 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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parents: 0
diff changeset
712 the local version of the preset (`--very-fast-local`). This is mutually
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parents: 0
diff changeset
713 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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parents: 0
diff changeset
714
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parents: 0
diff changeset
715 -----
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parents: 0
diff changeset
716
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parents: 0
diff changeset
717 **Scoring options**::
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parents: 0
diff changeset
718
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parents: 0
diff changeset
719 --ma &lt;int&gt;
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
720 Sets the match bonus. In `--local` mode `&lt;int&gt;` is added to the alignment
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
721 score for each position where a read character aligns to a reference character
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devteam
parents: 0
diff changeset
722 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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parents: 0
diff changeset
723
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parents: 0
diff changeset
724 --mp MX,MN
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parents: 0
diff changeset
725 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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devteam
parents: 0
diff changeset
726 number less than or equal to `MX` and greater than or equal to `MN` is
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parents: 0
diff changeset
727 subtracted from the alignment score for each position where a read character
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parents: 0
diff changeset
728 aligns to a reference character, the characters do not match, and neither is an
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parents: 0
diff changeset
729 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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parents: 0
diff changeset
730 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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parents: 0
diff changeset
731 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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parents: 0
diff changeset
732
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parents: 0
diff changeset
733 --np &lt;int&gt;
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parents: 0
diff changeset
734 Sets penalty for positions where the read, reference, or both, contain an
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parents: 0
diff changeset
735 ambiguous character such as `N`. Default: 1.
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parents: 0
diff changeset
736
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parents: 0
diff changeset
737 --rdg &lt;int1&gt;,&lt;int2&gt;
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parents: 0
diff changeset
738 Sets the read gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A read gap of
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devteam
parents: 0
diff changeset
739 length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default: 5, 3.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
740
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parents: 0
diff changeset
741 --rfg &lt;int1&gt;,&lt;int2&gt;
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parents: 0
diff changeset
742 Sets the reference gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A
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devteam
parents: 0
diff changeset
743 reference gap of length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default:
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parents: 0
diff changeset
744 5, 3.
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
745
2
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parents: 0
diff changeset
746 --score-min &lt;func&gt;
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devteam
parents: 0
diff changeset
747 Sets a function governing the minimum alignment score needed for an alignment to
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devteam
parents: 0
diff changeset
748 be considered "valid" (i.e. good enough to report). This is a function of read
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
749 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
750 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and
2
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devteam
parents: 0
diff changeset
751 the default in `--local` mode is `G,20,8`.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
752
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parents: 0
diff changeset
753 -----
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
754
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parents: 0
diff changeset
755 **Reporting options**::
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parents: 0
diff changeset
756
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parents: 0
diff changeset
757 -k &lt;int&gt;
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
758 By default, `bowtie2` searches for distinct, valid alignments for each read.
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
759 When it finds a valid alignment, it continues looking for alignments that are
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
760 nearly as good or better. The best alignment found is reported (randomly
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parents: 0
diff changeset
761 selected from among best if tied). Information about the best alignments is
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parents: 0
diff changeset
762 used to estimate mapping quality and to set SAM optional fields, such as
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devteam
parents: 0
diff changeset
763 `AS:i` and `XS:i`.
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parents: 0
diff changeset
764
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parents: 0
diff changeset
765 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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parents: 0
diff changeset
766 searches for at most `&lt;int&gt;` distinct, valid alignments for each read. The
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devteam
parents: 0
diff changeset
767 search terminates when it can't find more distinct valid alignments, or when it
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parents: 0
diff changeset
768 finds `&lt;int&gt;`, whichever happens first. All alignments found are reported in
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devteam
parents: 0
diff changeset
769 descending order by alignment score. The alignment score for a paired-end
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parents: 0
diff changeset
770 alignment equals the sum of the alignment scores of the individual mates. Each
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devteam
parents: 0
diff changeset
771 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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parents: 0
diff changeset
772 (which equals 256) set in its FLAGS field. For reads that have more than
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parents: 0
diff changeset
773 `&lt;int&gt;` distinct, valid alignments, `bowtie2` does not guarantee that the
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parents: 0
diff changeset
774 `&lt;int&gt;` alignments reported are the best possible in terms of alignment score.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
775 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
776
2
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parents: 0
diff changeset
777 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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parents: 0
diff changeset
778 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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parents: 0
diff changeset
779
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
780 -a
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parents: 0
diff changeset
781 Like `-k` but with no upper limit on number of alignments to search for. `-a`
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
782 is mutually exclusive with `-k`.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
783
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
784 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
785 aligning reads to long, repetitive genomes this mode can be very, very slow.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
786
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
787 -----
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
788
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
789 **Effort options**::
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parents: 0
diff changeset
790
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
791 -D &lt;int&gt;
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
792 Up to `&lt;int&gt;` consecutive seed extension attempts can "fail" before Bowtie 2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
793 moves on, using the alignments found so far. A seed extension "fails" if it
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parents: 0
diff changeset
794 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
795 automatically adjusted up when -k or -a are specified. Default: 15.
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parents: 0
diff changeset
796
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
797 -R &lt;int&gt;
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
798 `&lt;int&gt;` is the maximum number of times Bowtie 2 will "re-seed" reads with
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
799 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
800 (same length, same number of mismatches allowed) at different offsets and
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parents: 0
diff changeset
801 searches for more alignments. A read is considered to have repetitive seeds if
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parents: 0
diff changeset
802 the total number of seed hits divided by the number of seeds that aligned at
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parents: 0
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803 least once is greater than 300. Default: 2.
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parents: 0
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804
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parents: 0
diff changeset
805 -----
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parents: 0
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806
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parents: 0
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807 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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parents:
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808
2
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parents: 0
diff changeset
809 -I/--minins &lt;int&gt;
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parents: 0
diff changeset
810 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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parents: 0
diff changeset
811 specified and a paired-end alignment consists of two 20-bp alignments in the
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parents: 0
diff changeset
812 appropriate orientation with a 20-bp gap between them, that alignment is
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parents: 0
diff changeset
813 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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parents: 0
diff changeset
814 be valid in that case. If trimming options `-3` or `-5` are also used, the
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parents: 0
diff changeset
815 `-I` constraint is applied with respect to the untrimmed mates.
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parents: 0
diff changeset
816
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
817 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
818 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
819 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
820 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
821 efficient.
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parents: 0
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822
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parents: 0
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823 Default: 0 (essentially imposing no minimum)
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parents: 0
diff changeset
824
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parents: 0
diff changeset
825 -X/--maxins &lt;int&gt;
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parents: 0
diff changeset
826 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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parents: 0
diff changeset
827 is specified and a paired-end alignment consists of two 20-bp alignments in the
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parents: 0
diff changeset
828 proper orientation with a 60-bp gap between them, that alignment is considered
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
829 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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parents: 0
diff changeset
830 that case. If trimming options `-3` or `-5` are also used, the `-X`
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parents: 0
diff changeset
831 constraint is applied with respect to the untrimmed mates, not the trimmed
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parents: 0
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832 mates.
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parents: 0
diff changeset
833
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
834 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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parents: 0
diff changeset
835 run. This is because larger differences bewteen `-I` and `-X` require that
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parents: 0
diff changeset
836 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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devteam
parents: 0
diff changeset
837 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
838 efficient.
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parents: 0
diff changeset
839
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parents: 0
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840 Default: 500.
0
96d2e31a3938 Imported from capsule None
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parents:
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841
2
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parents: 0
diff changeset
842 --fr/--rf/--ff
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parents: 0
diff changeset
843 The upstream/downstream mate orientations for a valid paired-end alignment
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parents: 0
diff changeset
844 against the forward reference strand. E.g., if `--fr` is specified and there is
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parents: 0
diff changeset
845 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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parents: 0
diff changeset
846 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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parents: 0
diff changeset
847 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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parents: 0
diff changeset
848 complement of mate 1 and all other constraints are met, that too is valid.
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parents: 0
diff changeset
849 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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parents: 0
diff changeset
850 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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parents: 0
diff changeset
851 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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parents: 0
diff changeset
852 for Illumina's Paired-end Sequencing Assay).
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parents: 0
diff changeset
853
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parents: 0
diff changeset
854 --no-mixed
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parents: 0
diff changeset
855 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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parents: 0
diff changeset
856 a pair, it then tries to find alignments for the individual mates. This option
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parents: 0
diff changeset
857 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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parents:
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858
2
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parents: 0
diff changeset
859 --no-discordant
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parents: 0
diff changeset
860 By default, `bowtie2` looks for discordant alignments if it cannot find any
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
861 concordant alignments. A discordant alignment is an alignment where both mates
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parents: 0
diff changeset
862 align uniquely, but that does not satisfy the paired-end constraints
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parents: 0
diff changeset
863 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
864
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parents: 0
diff changeset
865 --dovetail
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
866 If the mates "dovetail", that is if one mate alignment extends past the
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parents: 0
diff changeset
867 beginning of the other such that the wrong mate begins upstream, consider that
3
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parents: 2
diff changeset
868 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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parents: 0
diff changeset
869
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parents: 0
diff changeset
870 --no-contain
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parents: 0
diff changeset
871 If one mate alignment contains the other, consider that to be non-concordant.
3
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parents: 2
diff changeset
872 Default: a mate can contain the other in a concordant alignment.
2
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parents: 0
diff changeset
873
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parents: 0
diff changeset
874 --no-overlap
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parents: 0
diff changeset
875 If one mate alignment overlaps the other at all, consider that to be
3
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parents: 2
diff changeset
876 non-concordant. Default: mates can overlap in a concordant alignment.
2
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parents: 0
diff changeset
877
0
96d2e31a3938 Imported from capsule None
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parents:
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878 ------
96d2e31a3938 Imported from capsule None
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parents:
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879
2
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parents: 0
diff changeset
880 **SAM options**::
0
96d2e31a3938 Imported from capsule None
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881
2
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diff changeset
882 --rg-id &lt;text&gt;
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parents: 0
diff changeset
883 Set the read group ID to `&lt;text&gt;`. This causes the SAM `@RG` header line to be
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parents: 0
diff changeset
884 printed, with `&lt;text&gt;` as the value associated with the `ID:` tag. It also
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parents: 0
diff changeset
885 causes the `RG:Z:` extra field to be attached to each SAM output record, with
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parents: 0
diff changeset
886 value set to `&lt;text&gt;`.
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
887
2
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parents: 0
diff changeset
888 --rg &lt;text&gt;
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parents: 0
diff changeset
889 Add `&lt;text&gt;` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
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parents: 0
diff changeset
890 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
ceb6467e276c Uploaded
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parents: 2
diff changeset
891 must also be specified. This is because the `ID` tag is required by the SAM
ceb6467e276c Uploaded
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parents: 2
diff changeset
892 Specification. Specify `--rg` multiple times to set multiple fields. See the
ceb6467e276c Uploaded
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parents: 2
diff changeset
893 SAM Specification for details about what fields are legal.
0
96d2e31a3938 Imported from capsule None
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parents:
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894
2
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parents: 0
diff changeset
895 --omit-sec-seq
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parents: 0
diff changeset
896 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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parents: 0
diff changeset
897 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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parents: 0
diff changeset
898 in those fields instead.
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parents: 0
diff changeset
899
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parents: 0
diff changeset
900 -----
0
96d2e31a3938 Imported from capsule None
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parents:
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901
2
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parents: 0
diff changeset
902 **Other options**::
0
96d2e31a3938 Imported from capsule None
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parents:
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903
2
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parents: 0
diff changeset
904 --reorder
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parents: 0
diff changeset
905 Guarantees that output SAM records are printed in an order corresponding to the
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parents: 0
diff changeset
906 order of the reads in the original input file, even when `-p` is set greater
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parents: 0
diff changeset
907 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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parents: 0
diff changeset
908 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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parents: 0
diff changeset
909 not specified. Has no effect if `-p` is set to 1, since output order will
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parents: 0
diff changeset
910 naturally correspond to input order in that case.
0
96d2e31a3938 Imported from capsule None
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parents:
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911
2
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parents: 0
diff changeset
912 --seed &lt;int&gt;
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parents: 0
diff changeset
913 Use `&lt;int&gt;` as the seed for pseudo-random number generator. Default: 0.
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
914
2
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parents: 0
diff changeset
915 --non-deterministic
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parents: 0
diff changeset
916 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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parents: 0
diff changeset
917 seeds the generator with a number derived from (a) the read name, (b) the
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parents: 0
diff changeset
918 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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parents: 0
diff changeset
919 option. This means that if two reads are identical (same name, same
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parents: 0
diff changeset
920 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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parents: 0
diff changeset
921 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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parents: 0
diff changeset
922 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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parents: 0
diff changeset
923 current time. This means that Bowtie 2 will not necessarily report the same
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parents: 0
diff changeset
924 alignment for two identical reads. This is counter-intuitive for some users,
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parents: 0
diff changeset
925 but might be more appropriate in situations where the input consists of many
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parents: 0
diff changeset
926 identical reads.
0
96d2e31a3938 Imported from capsule None
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parents:
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927
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
928 </help>
2
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parents: 0
diff changeset
929 <citations>
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parents: 0
diff changeset
930 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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parents: 0
diff changeset
931 <citation type="doi">10.1038/nmeth.1923</citation>
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parents: 0
diff changeset
932 </citations>
0
96d2e31a3938 Imported from capsule None
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parents:
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933 </tool>