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1 # RepeatExplorer2 with TAREAN (Tandem Repeat Analyzer) #
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2 -------------------------------------------------------------------------------
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3 New version of RepeatExplorer with TAndem REpeat ANalyzer
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4
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5 ## Authors
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6 Petr Novak, Jiri Macas, Pavel Neumann
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7 Biology Centre CAS, Czech Republic
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8
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9 ## Change log
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10
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11 [link](CHANGELOG.md)
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12
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13
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14
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15 ## Instalation ##
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16 To use RepeatExplorer without installation, We recommend to use our freely
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17 available galaxy server at
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18 [https://repeatexplorer-elixir.cerit-sc.cz](https://repeatexplorer-elixir.cerit-sc.cz).
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19 This server is provided in frame of ELIXIR-CZ project. Additionally, the galaxy
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20 server includs also additional tools useful data preprocessing, quality contraol
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21 and genome annotation.
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22
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23 For command line version from standalone installation, follow the instruction below:
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24
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25
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26 To download source using git command:
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27
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28 git clone https://bitbucket.org/petrnovak/repex_tarean.git
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29 cd repex_tarean
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30
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31 We recommend to install dependencies using conda (conda can be installed using [miniconda](https://docs.conda.io/en/latest/miniconda.html)). The required environment can be prepared using command:
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32
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33 conda env create -f environment.yml
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34
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35 activate prepared environment using:
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36
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37 conda activate repeatexplorer
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38
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39 In the `repex_tarean` direcory compile source and prepare databases using:
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40
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41 make
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42
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43 Support for 32-bit executables is required. If you are using Ubuntu distribution you can add 32-bit support by running:
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44
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45 sudo dpkg --add-architecture i386
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46 sudo apt-get update
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47 sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386
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48
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49
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50 to verify installation you can run clustering on example data:
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51
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52 ./seqclust -p -v tmp/clustering_output test_data/LAS_paired_10k.fas
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53
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54
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55 ## Protein databases
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56
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57 Repeatexplorer2 utilize REXdb database of protein domains for repeat annotation and classification. Structure of database is described on [http://repeatexplorer.org/](http://repeatexplorer.org/). Current version of database for repeatexplorer is fetched from bitbucket repository [https://bitbucket.org/petrnovak/re_databases]https://bitbucket.org/petrnovak/re_databases() during compilation using make command
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58
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59
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60 ## RepeatExplorer command line options
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61
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62 usage: seqclust [-h] [-p] [-A] [-t] [-l LOGFILE] [-m {float range 0.0..100.0}]
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63 [-M {0,float range 0.1..1}] [-o {float range 30.0..80.0}]
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64 [-c CPU] [-s SAMPLE] [-P PREFIX_LENGTH] [-v OUTPUT_DIR]
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65 [-r MAX_MEMORY] [-d DATABASE DATABASE] [-C] [-k]
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66 [-a {2,3,4,5}]
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67 [-tax {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}]
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68 [-opt {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}]
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69 [-D {BLASTX_W2,BLASTX_W3,DIAMOND}]
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70 sequences
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71
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72 RepeatExplorer:
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73 Repetitive sequence discovery and clasification from NGS data
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74
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75
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76
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77 positional arguments:
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78 sequences
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79
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80 optional arguments:
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81 -h, --help show this help message and exit
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82 -p, --paired
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83 -A, --automatic_filtering
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84 -t, --tarean_mode analyze only tandem reapeats without additional classification
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85 -l LOGFILE, --logfile LOGFILE
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86 log file, logging goes to stdout if not defines
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87 -m {float range 0.0..100.0}, --mincl {float range 0.0..100.0}
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88 -M {0,float range 0.1..1}, --merge_threshold {0,float range 0.1..1}
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89 threshold for mate-pair based cluster merging, default 0 - no merging
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90 -o {float range 30.0..80.0}, --min_lcov {float range 30.0..80.0}
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91 minimal overlap coverage - relative to longer sequence length, default 55
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92 -c CPU, --cpu CPU number of cpu to use, if 0 use max available
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93 -s SAMPLE, --sample SAMPLE
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94 use only sample of input data[by default max reads is used
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95 -P PREFIX_LENGTH, --prefix_length PREFIX_LENGTH
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96 If you wish to keep part of the sequences name,
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97 enter the number of characters which should be
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98 kept (1-10) instead of zero. Use this setting if
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99 you are doing comparative analysis
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100 -v OUTPUT_DIR, --output_dir OUTPUT_DIR
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101 -r MAX_MEMORY, --max_memory MAX_MEMORY
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102 Maximal amount of available RAM in kB if not set
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103 clustering tries to use whole available RAM
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104 -d DATABASE DATABASE, --database DATABASE DATABASE
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105 fasta file with database for annotation and name of database
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106 -C, --cleanup remove unncessary large files from working directory
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107 -k, --keep_names keep sequence names, by default sequences are renamed
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108 -a {2,3,4,5}, --assembly_min {2,3,4,5}
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109 Assembly is performed on individual clusters, by default
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110 clusters with size less then 5 are not assembled. If you
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111 want need assembly of smaller cluster set *assmbly_min*
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112 accordingly
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113 -tax {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}, --taxon {VIRIDIPLANTAE3.0,VIRIDIPLANTAE2.2,METAZOA2.0,METAZOA3.0}
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114 Select taxon and protein database version
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115 -opt {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}, --options {ILLUMINA,ILLUMINA_DUST_OFF,ILLUMINA_SHORT,OXFORD_NANOPORE}
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116 -D {BLASTX_W2,BLASTX_W3,DIAMOND}, --domain_search {BLASTX_W2,BLASTX_W3,DIAMOND}
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117 Detection of protein domains can be performed by either blastx or
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118 diamond" program. options are:
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119 BLASTX_W2 - blastx with word size 2 (slowest, the most sesitive)
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120 BLASTX_W3 - blastx with word size 3 (default)
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121 DIAMOND - diamond program (significantly faster, less sensitive)
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122 To use this option diamond program must be installed in your PATH
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123
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124
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125
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126 ## Galaxy toolshed
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127 TODO
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128
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129 ## Reproducibility
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130 To make clustering reproducible between runs with the
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131 same data, environment variable PYTHONHASHSEED must be set:
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132
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133 export PYTHONHASHSEED=0
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134
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135 ## Disk space requirements
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136 Large sqlite database for temporal data is created in OS specific temp directory- usually /tmp/
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137 To use alternative location, it is necessary specify `TEMP` environment variable.
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138
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139 ## CPU and RAM requirements
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140
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141 Resources requirements can be set either from command line arguments `--max-memory` and `--cpu` or
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142 using environment variables `TAREAN_MAX_MEM` and `TAREAN_CPU`. If not set, pipeline use all
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143 available resources
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144
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145 ## How cite
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146
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147 If you use RepeatExplorer for general repeat characterization in your work please cite:
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148
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149 - [Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence read. Bioinformatics 29:792-793](http://bioinformatics.oxfordjournals.org/content/29/6/792)
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150
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151 or
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152
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153 - [Novak, P., Neumann, P., Macas, J. (2010) - Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics 11 :37](http://www.biomedcentral.com/1471-2105/11/378)
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154
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155 If you use TAREAN for satellite detection and characterization please cite:
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156
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157 - [Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acid Research](https://doi.org/10.1093/nar/gkx257)
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