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1 <tool id="lastz_wrapper_2" name="Lastz" version="1.2.2">
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2 <description> map short reads against reference sequence</description>
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3 <command interpreter="python">lastz_wrapper.py
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4 #if $seq_name.how_to_name=="yes":
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5 --ref_name=$seq_name.ref_name
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6 #end if
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7 --ref_source=$source.ref_source
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8 --source_select=$params.source_select
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9 --out_format=$out_format
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10 --input2=$input2
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11 #if $source.ref_source=="history":
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12 --input1=$source.input1
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13 --ref_sequences=$input1.metadata.sequences
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14 #else:
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15 --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }"
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16 --ref_sequences="None"
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17 #end if
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18 #if $params.source_select=="pre_set":
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19 --pre_set_options=${params.pre_set_options}
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20 #else:
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21 --strand=$params.strand
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22 --seed=$params.seed
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23 --gfextend=$params.gfextend
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24 --chain=$params.chain
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25 --transition="$params.transition"
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26 --O=$params.O
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27 --E=$params.E
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28 --X=$params.X
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29 --Y=$params.Y
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30 --K=$params.K
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31 --L=$params.L
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32 --entropy=$params.entropy
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33 #end if
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34 --identity_min=$min_ident
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35 --identity_max=$max_ident
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36 --coverage=$min_cvrg
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37 --output=$output1
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38 --unmask=$unmask
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39 --lastzSeqsFileDir=${GALAXY_DATA_INDEX_DIR}
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40 </command>
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41 <inputs>
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42 <param name="input2" format="fasta" type="data" label="Align sequencing reads in" />
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43 <conditional name="source">
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44 <param name="ref_source" type="select" label="Against reference sequences that are">
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45 <option value="cached">locally cached</option>
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46 <option value="history">in your history</option>
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47 </param>
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48 <when value="cached">
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49 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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50 <options from_data_table="lastz_seqs" />
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51 </param>
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52 </when>
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53 <when value="history">
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54 <param name="input1" type="data" format="fasta" label="Select a reference dataset" />
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55 </when>
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56 </conditional>
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57 <param name="out_format" type="select" label="Output format">
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58 <option value="sam">SAM</option>
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59 <option value="diffs">Polymorphisms</option>
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60 <option value="tabular">Tabular</option>
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61 </param>
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62 <conditional name="params">
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63 <param name="source_select" type="select" label="Lastz settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
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64 <option value="pre_set">Commonly used</option>
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65 <option value="full">Full Parameter List</option>
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66 </param>
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67 <when value="pre_set">
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68 <param name="pre_set_options" type="select" label="Select mapping mode">
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69 <option value="yasra98">Roche-454 98% identity</option>
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70 <option value="yasra95">Roche-454 95% identity</option>
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71 <option value="yasra90">Roche-454 90% identity</option>
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72 <option value="yasra85">Roche-454 85% identity</option>
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73 <option value="yasra75">Roche-454 75% identity</option>
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74 <option value="yasra95short">Illumina 95% identity</option>
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75 <option value="yasra85short">Illumina 85% identity</option>
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76 </param>
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77 </when>
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78 <when value="full">
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79 <param name="strand" type="select" label="Which strand to search?">
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80 <option value="both">Both</option>
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81 <option value="plus">Search forward strand only (the one in the reference)</option>
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82 <option value="minus">Search the reverse complement strand only (opposite of the reference)</option>
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83 </param>
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84 <param name="seed" type="select" label="Select seeding settings" help="allows you set word size and number of mismatches">
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85 <option value="12of19">Seed hits require a 19 bp word with matches in 12 specific positions</option>
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86 <option value="14of22">Seed hits require a 22 bp word with matches in 14 specific positions</option>
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87 </param>
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88 <param name="transition" type="select" label="Select transition settings" help="affects the number of allowed transition substitutions">
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89 <option value="transition">Allow one transition in each seed hit</option>
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90 <option value="transition=2">Allow two transitions in a seed hit </option>
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91 <option value="notransition">Don't allow any transitions in seed hits</option>
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92 </param>
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93 <param name="gfextend" type="select" label="Perform gap-free extension of seed hits to HSPs (high scoring segment pairs)?">
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94 <option value="nogfextend">No</option>
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95 <option value="gfextend">Yes</option>
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96 </param>
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97 <param name="chain" type="select" label="Perform chaining of HSPs?">
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98 <option value="nochain">No</option>
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99 <option value="chain">Yes</option>
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100 </param>
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101 <param name="O" type="integer" size="5" value="400" label="Gap opening penalty"/>
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102 <param name="E" type="integer" size="5" value="30" label="Gap extension penalty"/>
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103 <param name="X" type="integer" size="5" value="910" label="X-drop threshold"/>
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104 <param name="Y" type="integer" size="5" value="9370" label="Y-drop threshold"/>
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105 <param name="K" type="integer" size="5" value="3000" label="Set the threshold for HSPs (ungapped extensions scoring lower are discarded)"/>
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106 <param name="L" type="integer" size="5" value="3000" label="Set the threshold for gapped alignments (gapped extensions scoring lower are discarded)"/>
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107 <param name="entropy" type="select" label="Involve entropy when filtering HSPs?">
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108 <option value="noentropy">No</option>
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109 <option value="entropy">Yes</option>
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110 </param>
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111 </when>
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112 </conditional>
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113 <conditional name="seq_name">
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114 <param name="how_to_name" type="select" label="Do you want to modify the reference name?">
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115 <option value="no">No</option>
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116 <option value="yes">Yes</option>
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117 </param>
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118 <when value="yes">
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119 <param name="ref_name" type="text" size="25" value="Type sequence name here" label="Enter name for the Reference sequence"/>
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120 </when>
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121 <when value="no" />
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122 </conditional>
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123 <param name="min_ident" type="integer" size="3" value="0" label="Do not report matches below this identity (%)"/>
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124 <param name="max_ident" type="integer" size="3" value="100" label="Do not report matches above this identity (%)"/>
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125 <param name="min_cvrg" type="integer" size="3" value="0" label="Do not report matches that cover less than this percentage of each read"/>
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126 <param name="unmask" type="select" label="Convert lowercase bases to uppercase">
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127 <option value="yes">Yes</option>
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128 <option value="no">No</option>
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129 </param>
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130 </inputs>
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131 <outputs>
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132 <data format="tabular" name="output1" label="${tool.name} on ${on_string}: mapped reads">
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133 <change_format>
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134 <when input="out_format" value="sam" format="sam" />
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135 </change_format>
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136 </data>
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137 </outputs>
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138 <requirements>
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139 <requirement type="package">lastz</requirement>
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140 </requirements>
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141 <tests>
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142 <test>
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143 <!--
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144 Lastz command:
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145 lastz phiX.2bit/phiX174[nickname=Ref] test-data/b1.fasta +nogfextend +nochain +gapped +strand=both +seed=12of19 +transition O=400 E=30 X=910 Y=9370 K=3000 L=3000 +noentropy +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=sam- > lastz_wrapper_out2.sam
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146 You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data. You will have to replace all the pluses before the
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147 commands with 2 dashes, as double-dash can't appear in an XML comment.
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148 -->
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149 <param name="input2" value="b1.fasta" ftype="fasta" />
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150 <param name="ref_source" value="cached" />
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151 <!-- this is the backwards-compatible "unique value" for this file, not an actual path -->
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152 <param name="input1_2bit" value="/galaxy/data/phiX/seq/phiX.2bit" />
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153 <param name="out_format" value="sam" />
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154 <param name="source_select" value="full" />
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155 <param name="strand" value="both" />
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156 <param name="seed" value="12of19" />
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157 <param name="transition" value="transition" />
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158 <param name="gfextend" value="nogfextend" />
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159 <param name="chain" value="nochain" />
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160 <param name="O" value="400" />
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161 <param name="E" value="30" />
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162 <param name="X" value="910" />
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163 <param name="Y" value="9370" />
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164 <param name="K" value="3000" />
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165 <param name="L" value="3000" />
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166 <param name="entropy" value="noentropy" />
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167 <!--
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168 how_to_name is not the default. It is changed to modify
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169 input1_2bit by adding the ref_name as a nickname
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170 -->
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171 <param name="how_to_name" value="yes" />
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172 <param name="ref_name" value="Ref" />
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173 <param name="min_ident" value="0" />
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174 <param name="max_ident" value="100" />
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175 <param name="min_cvrg" value="0" />
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176 <param name="unmask" value="yes" />
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177 <output name="output1" file="lastz_wrapper_out2.sam" />
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178 </test>
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179 <test>
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180 <!--
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181 Lastz command:
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182 lastz test-data/phiX.fasta test-data/b1.fasta[fullnames] +yasra95short +ambiguousn +nolaj +identity=0..100 +coverage=0 +format=diffs > lastz_wrapper_out3.tabular
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183 phiX.fasta and b1.fasta are located in galaxy's test-data. You will have to replace all the pluses before the commands with 2 dashes,
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184 as double-dash can't appear in an XML comment.
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185 -->
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186 <param name="input2" value="b1.fasta" ftype="fasta" />
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187 <param name="ref_source" value="history" />
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188 <param name="input1" value="phiX.fasta" ftype="fasta" />
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189 <param name="out_format" value="diffs" />
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190 <param name="source_select" value="pre_set" />
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191 <param name="pre_set_options" value="yasra95short" />
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192 <param name="how_to_name" value="no" />
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193 <param name="min_ident" value="0" />
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194 <param name="max_ident" value="100" />
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195 <param name="min_cvrg" value="0" />
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196 <param name="unmask" value="yes" />
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197 <output name="output1" file="lastz_wrapper_out3.tabular" />
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198 </test>
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199 <test>
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200 <!--
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201 Lastz command: first you will need to split the file phiX_split.fasta into two files,
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202 phiX1.fasta and phiX2.fasta, each with 1 sequence (phiX1 and phiX2, respectively). Then:
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203 lastz phiX1.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle > lastz_wrapper_out4.tabular
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204 lastz phiX2.fasta test-data/b1.fasta *yasra95short *ambiguousn *nolaj *identity=0..100 *coverage=0 *format=general-:score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle >> lastz_wrapper_out4.tabular
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205 You need to point to phiX1.fasta and phiX2.fasta somewhere on your system.
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206 phiX_split.fasta and b1.fasta are located in galaxy's test-data
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207 You will have to replace all the asterisks before the commands with 2 dashes,
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208 as double-dash can't appear in an XML comment
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209
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210 NOTE: since the input file include more than 1 sequence, the output must be sorted in
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211 order for functional test to pass. This is done using the sort="True" attribute on the output.
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212 -->
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213 <param name="input2" value="b1.fasta" ftype="fasta" />
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214 <param name="ref_source" value="history" />
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215 <param name="input1" value="phiX_split.fasta" ftype="fasta" />
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216 <param name="out_format" value="tabular" />
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217 <param name="source_select" value="pre_set" />
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218 <param name="pre_set_options" value="yasra95short" />
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219 <param name="how_to_name" value="no" />
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220 <param name="min_ident" value="0" />
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221 <param name="max_ident" value="100" />
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222 <param name="min_cvrg" value="0" />
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223 <param name="unmask" value="yes" />
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224 <output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />
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225 </test>
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226 </tests>
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227 <help>
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228
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229 **What it does**
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230
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231 **LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.
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232
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233 .. _here: http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00.html
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234
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235 ------
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236
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237 **Input formats**
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238
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239 LASTZ accepts reference and reads in FASTA format. However, because Galaxy supports implicit format conversion the tool will recognize fastq and other method specific formats.
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240
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241 ------
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242
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243 **Outputs**
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244
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245 LASTZ generates one output. Depending on the choice you make in the *Select output format* drop-down, LASTZ will produce a SAM file showing sequence alignments, a list of differences between the reads and reference (Polymorphisms), or a general table with one line per alignment block (Tabular). Examples of these outputs are shown below.
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246
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247 **SAM output**
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248
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249 SAM has 12 columns::
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250
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251 1 2 3 4 5 6 7 8 9 10 11 12
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252 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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253 HWI-EAS91_1_30788AAXX:1:2:1670:915 99 chr9 58119878 60 36M = 58120234 392 GACCCCTACCCCACCGTGCTCTGGATCTCAGTGTTT IIIIIIIIIIIIIIIIEIIIIIII7IIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
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254 HWI-EAS91_1_30788AAXX:1:2:1670:915 147 chr9 58120234 60 36M = 58119878 -392 ATGAGTCGAATTCTATTTTCCAAACTGTTAACAAAA IFIIDI;IIICIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
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255
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256
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257 where::
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258
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259 Column Description
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260 --------- ---------------------------------------------------------------------
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261 1. QNAME Query (pair) NAME
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262 2. FLAG bitwise FLAG
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263 3. RNAME Reference sequence NAME
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264 4. POS 1-based leftmost POSition/coordinate of clipped sequence
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265 5. MAPQ MAPping Quality (Phred-scaled)
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266 6. CIGAR extended CIGAR string
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267 7. MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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268 8. MPOS 1-based Mate POSition
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269 9. ISIZE Inferred insert SIZE
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270 10. SEQ query SEQuence on the same strand as the reference
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271 11. QUAL query QUALity (ASCII-33 gives the Phred base quality)
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272 12. OPT variable OPTional fields in the format TAG:VTYPE:VALUE, tab-separated
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273
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274 The flags are as follows::
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275
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276 Flag Description
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277 ------ -------------------------------------
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278 0x0001 the read is paired in sequencing
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279 0x0002 the read is mapped in a proper pair
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280 0x0004 the query sequence itself is unmapped
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281 0x0008 the mate is unmapped
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282 0x0010 strand of the query (1 for reverse)
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283 0x0020 strand of the mate
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284 0x0040 the read is the first read in a pair
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285 0x0080 the read is the second read in a pair
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286 0x0100 the alignment is not primary
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287
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288 **Polymorphism (SNP or differences) output**
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289
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290 Polymorphism output contains 14 columns::
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291
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292 1 2 3 4 5 6 7 8 9 10 11 12 13 14
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293 --------------------------------------------------------------------------------------------------------------------------------------------------------------
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294 chrM 2490 2491 + 5386 HWI-EAS91_1_306UPAAXX:6:1:486:822 10 11 - 36 C A ACCTGTTTTACAGACACCTAAAGCTACATCGTCAAC ACCTGTTTTAAAGACACCTAAAGCTACATCGTCAAC
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295 chrM 2173 2174 + 5386 HWI-EAS91_1_306UPAAXX:6:1:259:1389 26 27 + 36 G T GCGTACTTATTCGCCACCATGATTATGACCAGTGTT GCGTACTTATTCGCCACCATGATTATTACCAGTGTT
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296
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297 where::
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298
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299 1. (chrM) - Reference sequence id
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300 2. (2490) - Start position of the difference in the reference
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301 3. (2491) - End position of the difference in the reference
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302 4. (+) - Strand of the reference (always plus)
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303 5. (5386) - Length of the reference sequence
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304 6. (HWI...) - read id
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305 7. (10) - Start position of the difference in the read
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306 8. (11) - End position of the difference in the read
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307 9. (+) - Strand of the read
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308 10. (36) - Length of the read
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309 11. (C) - Nucleotide in the reference
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310 12. (A) - Nucleotide in the read
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311 13. (ACC...) - Reference side os the alignment
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312 14. (ACC...) - Read side of the alignment
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313
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314 **Tabular output**
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315
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316 Tabular output is a tab-separated format with 30 columns::
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317
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318 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
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319 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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320 14 PHIX174 + 5386 4648 4647 4661 14 ATTTTCGTGATATT EYKX4VC01BV8HS + 204 154 153 167 154 153 167 14 ATTTTCGTGATATT .............. 14M 14/14 100.0% 14/204 6.9% 0/14 0.0% 4494 NA
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321 16 PHIX174 + 5386 3363 3362 3378 16 GACGCCGGATTTGAGA EYKX4VC01AWJ88 - 259 36 35 51 209 208 224 16 GACGCCGGATTTGAGA ................ 16M 16/16 100.0% 16/259 6.2% 0/16 0.0% 3327 NA
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322
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323 The following columns are present::
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324
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325 Field Meaning
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326 ---------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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327 1. score Score of the alignment block. The scale and meaning of this number will vary, depending on the final stage performed and other command-line options.
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328 2. name1 Name of the target sequence.
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329 3. strand1 Target sequence strand, either "+" or "−".
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330 4. size1 Size of the entire target sequence.
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331 5. start1 Starting position of the alignment block in the target, origin-one.
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332 6. zstart1 Starting position of the alignment block in the target, origin-zero.
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333 7. end1 Ending position of the alignment block in the target, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
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334 8. length1 Length of the alignment block in the target (excluding gaps).
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335 9. text1 Aligned characters in the target, including gap characters.
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336 10. name2 Name of the query sequence.
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337 11. strand2 Query sequence strand, either "+" or "−".
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338 12. size2 Size of the entire query sequence.
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339 13. start2 Starting position of the alignment block in the query, origin-one.
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340 14. zstart2 Starting position of the alignment block in the query, origin-zero.
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341 15. end2 Ending position of the alignment block in the query, expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems).
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342 16. start2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-one. Note that if strand2 is "−", then this is the other end of the block from start2.
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343 17. zstart2+ Starting position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), origin-zero. Note that if strand2 is "−", then this is the other end of the block from zstart2.
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344 18. end2+ Ending position of the alignment block in the query, counting along the query sequence's positive strand (regardless of which query strand was aligned), expressed either as origin-one closed or origin-zero half-open (the ending value is the same in both systems). Note that if strand2 is "−", then this is the other end of the block from end2.
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345 19. length2 Length of the alignment block in the query (excluding gaps).
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346 20. text2 Aligned characters in the query, including gap characters.
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347 21. diff Differences between what would be written for text1 and text2. Matches are written as . (period), transitions as : (colon), transversions as X, and gaps as - (hyphen).
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348 22. cigar A CIGAR-like representation of the alignment's path through the Dynamic Programming matrix. This is the short representation, without spaces, described in the Ensembl CIGAR specification.
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349 23./24. identity Fraction of aligned bases in the block that are matches (see Identity). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
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350 25./26. coverage Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (see Coverage). This is written as two fields. The first field is a fraction, written as <n>/<d>. The second field contains the same value, computed as a percentage.
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351 27./28. gaprate Rate of gaps (also called indels) in the alignment block. This is written as two fields. The first field is a fraction, written as <n>/<d>, with the numerator being the number of alignment columns containing gaps and the denominator being the number without gaps. The second field contains the same value, computed as a percentage.
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352 29. diagonal The diagonal of the start of the alignment block in the dynamic programming matrix, expressed as an identifying number start1-start2.
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353 30. shingle A measurement of the shingle overlap between the target and the query. This is intended for the case where both the target and query are relatively short, and their ends are expected to overlap.
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354
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355 -------
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356
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357 **LASTZ Settings**
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358
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359 There are two setting modes: (1) **Commonly used settings** and (2) **Full Parameter List**.
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360
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361 **Commonly used settings**
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362
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363 There are seven modes::
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364
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365 Illumina-Solexa/AB-SOLiD 95% identity
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366 Illumina-Solexa/AB-SOLiD 85% identity
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367 Roche-454 98% identity
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368 Roche-454 95% identity
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369 Roche-454 90% identity
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370 Roche-454 85% identity
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371 Roche-454 75% identity
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372
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373 When deciding which one to use, consider the following: a 36 bp read with two differences will be 34/36 = 94% identical to the reference.
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374
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375 **Full Parameter List**
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376
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377 This mode gives you fuller control over lastz. The description of these and other parameters is found at the end of this page. Note that not all parameters are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu.
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378
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379 ------
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380
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381 **Do you want to modify the reference name?**
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382
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383 This option allows you to set the name of the reference sequence manually. This is helpful when, for example, you would like to make the reference name compatible with the UCSC naming conventions to be able to display your lastz results as a custom track at the UCSC Genome Browser.
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384
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385 ------
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386
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387 **LASTZ parameter list**
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388
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389 This is an exhaustive list of LASTZ options. Once again, please note that not all options are included in this interface. If you would like to make additional options available through Galaxy, e-mail us at galaxy-bugs@bx.psu.edu::
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390
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391 target[[s..e]][-] spec/file containing target sequence (fasta or nib)
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392 [s..e] defines a subrange of the file
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393 - indicates reverse-complement
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394 (use --help=files for more details)
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395 query[[s..e]][-] spec/file containing query sequences (fasta or nib)
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396 if absent, queries come from stdin (unless they
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397 aren't needed, as for --self or --tableonly)
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398 (use --help=files for more details)
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399 --self the target sequence is also the query
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400 --quantum the query sequence contains quantum DNA
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401 --seed=match<length> use a word with no gaps instead of a seed pattern
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402 --seed=half<length> use space-free half-weight word instead of seed pattern
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403 --match=<reward>[,<penalty>] set the score values for a match (+<reward>)
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404 and mismatch (-<penalty>)
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405 --[no]trans[ition][=2] allow one or two transitions in a seed hit
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406 (by default a transition is allowed)
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407 --word=<bits> set max bits for word hash; use this to trade time for
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408 memory, eliminating thrashing for heavy seeds
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409 (default is 28 bits)
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410 --[no]filter=[<T>:]<M> filter half-weight seed hits, requiring at least M
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411 matches and allowing no more than T transversions
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412 (default is no filtering)
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413 --notwins require just one seed hit
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414 --twins=[<min>:]<maxgap> require two nearby seed hits on the same diagonal
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415 (default is twins aren't required)
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416 --notwins allow single, isolated seeds
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417 --[no]recoverseeds avoid losing seeds in hash collisions. Cannot be used with --twins
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418 --seedqueue=<entries> set number of entries in seed hit queue
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419 (default is 262144)
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420 --anchors=<file> read anchors from a file, instead of discovering anchors
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421 via seeding
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422 --recoverhits recover hash-collision seed hits
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423 (default is not to recover seed hits)
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424 --step=<length> set step length (default is 1)
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425 --maxwordcount=<limit> words occurring more often than <limit> in the target
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426 are not eligible for seeds
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427 --strand=both search both strands
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428 --strand=plus search + strand only (matching strand of query spec)
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429 --strand=minus search - strand only (opposite strand of query spec)
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430 (by default both strands are searched)
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431 --ambiguousn treat N as an ambiguous nucleotide
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432 (by default N is treated as a sequence splicing character)
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433 --[no]gfextend perform gap-free extension of seed hits to HSPs
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434 (by default no extension is performed)
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435 --[no]chain perform chaining
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436 --chain=<diag,anti> perform chaining with given penalties for diagonal and
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437 anti-diagonal
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438 (by default no chaining is performed)
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439 --[no]gapped perform gapped alignment (instead of gap-free)
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|
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440 (by default gapped alignment is performed)
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|
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441 --score[s]=<file> read substitution scores from a file
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442 (default is HOXD70)
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443 --unitscore[s] scores are +1/-1 for match/mismatch
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444 --gap=<[open,]extend> set gap open and extend penalties (default is 400,30)
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445 --xdrop=<score> set x-drop threshold (default is 10*sub[A][A])
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446 --ydrop=<score> set y-drop threshold (default is open+300extend)
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447 --infer[=<control>] infer scores from the sequences, then use them
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448 --inferonly[=<control>] infer scores, but don't use them (requires --infscores)
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|
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449 all inference options are read from the control file
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|
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450 --infscores[=<file>] write inferred scores to a file
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|
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451 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
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|
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452 ungapped extensions scoring lower are discarded
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|
|
453 <score> can also be a percentage or base count
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|
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454 --entropy adjust for entropy when qualifying HSPs in the x-drop extension
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|
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455 method
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|
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456 --noentropy don't adjust for entropy when qualifying HSPs
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|
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457 --exact=<length> set threshold for exact matches
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|
|
458 if specified, exact matches are found rather than high
|
|
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459 scoring pairs (replaces --hspthresh)
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|
|
460 --inner=<score> set threshold for HSPs during interpolation
|
|
|
461 (default is no interpolation)
|
|
|
462 --gappedthresh=<score> set threshold for gapped alignments
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|
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463 gapped extensions scoring lower are discarded
|
|
|
464 <score> can also be a percentage or base count
|
|
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465 (default is to use same value as --hspthresh)
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466 --ball=<score> set minimum score required of words 'in' a quantum ball
|
|
|
467 --[no]entropy involve entropy in filtering high scoring pairs
|
|
|
468 (default is "entropy")
|
|
|
469 --[no]mirror report/use mirror image of all gap-free alignments
|
|
|
470 (default is "mirror" for self-alignments only)
|
|
|
471 --traceback=<bytes> space for trace-back information
|
|
|
472 (default is 80.0M)
|
|
|
473 --masking=<count> mask any position in target hit this many times
|
|
|
474 zero indicates no masking
|
|
|
475 (default is no masking)
|
|
|
476 --targetcapsule=<capsule_file> the target seed word position table and seed
|
|
|
477 (as well as the target sequence)are read from specified file
|
|
|
478 --segments=<segment_file> read segments from a file, instead of discovering
|
|
|
479 them via seeding. Replaces other seeding or gap-free extension
|
|
|
480 options
|
|
|
481 --[no]census[=<file>] count/report how many times each target base aligns
|
|
|
482 (default is to not report census)
|
|
|
483 --identity=<min>[..<max>] filter alignments by percent identity
|
|
|
484 0<=min<=max<=100; blocks (or HSPs) outside min..max
|
|
|
485 are discarded
|
|
|
486 (default is no identity filtering)
|
|
|
487 --coverage=<min>[..<max>] filter alignments by percentage pf query covered
|
|
|
488 0<=min<=max<=100; blocks (or HSPs) outside min..max
|
|
|
489 are discarded
|
|
|
490 (default is no query coverage filtering)
|
|
|
491 --notrivial do not output trivial self-alignment block if the target and query
|
|
|
492 sequences are identical. Using --self enables this option automatically
|
|
|
493 --output=<output_file> write the alignments to the specified file name instead of stdout
|
|
|
494 --code=<file> give quantum code for query sequence (only for display)
|
|
|
495 --format=<type> specify output format; one of lav, axt, maf, maf+, maf-, text,
|
|
|
496 lav+text, cigar, text, rdplot, general, or general:<fields>
|
|
|
497 (by default output is LAV)
|
|
|
498 --rdotplot=<file> create an additional output file suitable for plotting the alignments
|
|
|
499 with the R statistical package.
|
|
|
500 --markend Just before normal completion, write "# lastz end-of-file" to output file
|
|
|
501 --census[=<output_file>] count and report how many times each target base aligns, up
|
|
|
502 to 255. Ns are included in the count
|
|
|
503 --census16[=<output_file>] count and report how many times each target base aligns, up
|
|
|
504 up 65 thousand
|
|
|
505 --census32[=<output_file>] count and report how many times each target bas aligns, up
|
|
|
506 to 4 billion
|
|
|
507 --writecapsule=<capsule_file> just write out a target capsule file and quit; don't
|
|
|
508 search for seeds or perform subsequent stages
|
|
|
509 --verbosity=<level> set info level (0 is minimum, 10 is everything)
|
|
|
510 (default is 0)
|
|
|
511 --[no]runtime report runtime in the output file
|
|
|
512 (default is to not report runtime)
|
|
|
513 --tableonly[=count] just produce the target position table, don't
|
|
|
514 search for seeds
|
|
|
515 --[no]stats[=<file>] show search statistics (or don't)
|
|
|
516 (not available in this build)
|
|
|
517 --version report the program version and quit
|
|
|
518 --help list all options
|
|
|
519 --help=files list information about file specifiers
|
|
|
520 --help=short[cuts] list blastz-compatible shortcuts
|
|
|
521 --help=yasra list yasra-specific shortcuts
|
|
|
522
|
|
|
523 </help>
|
|
|
524 </tool>
|
