annotate repex_tarean.xml @ 5:5e592edbad95 draft

Uploaded
author petr-novak
date Wed, 29 Apr 2020 09:41:55 -0400
parents d89d4fa8a17b
children ed5a72d4693d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
1 <tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8" >
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
2 <stdio>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
3 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
4 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
5 <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
6 <exit_code range="1:" level="fatal" description="Error" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
7 </stdio>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
8 <description>Identification of genomic tandem repeats from NGS data</description>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
9 <requirements>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
10 <requirement type="package">imagemagick</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
11 <requirement type="package">mafft</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
12 <requirement type="package">blast</requirement>
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
13 <requirement type="package" version="0.9.29">diamond</requirement>
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
14 <requirement type="package">blast-legacy</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
15 <requirement type="package">r-igraph</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
16 <requirement type="package">r-data.tree</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
17 <requirement type="package">r-stringr</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
18 <requirement type="package">r-r2html</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
19 <requirement type="package">r-hwriter</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
20 <requirement type="package">r-dt</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
21 <requirement type="package">r-scales</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
22 <requirement type="package">r-plotrix</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
23 <requirement type="package">r-png</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
24 <requirement type="package">r-plyr</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
25 <requirement type="package">r-dplyr</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
26 <requirement type="package">r-optparse</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
27 <requirement type="package">r-dbi</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
28 <requirement type="package">r-rsqlite</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
29 <requirement type="package">r-rserve</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
30 <requirement type="package">bioconductor-biostrings</requirement>
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
31 <requirement type="package" version="2.3.8">repex_tarean</requirement>
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
32 <requirement type="set_environment">REPEX</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
33 <requirement type="set_environment">REPEX_VERSION</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
34 <requirement type="package" version="0.9.1">pyrserve</requirement>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
35 </requirements>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
36 <command detect_errors="exit_code">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
37 export PYTHONHASHSEED=0;
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
38 \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
39 #if $advanced_options.advanced:
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
40 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
41 #if $advanced_options.custom_library.options_custom_library :
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
42 -d $advanced_options.custom_library.library extra_database
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
43 #end if
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
44 #if $advanced_options.options.options:
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
45 -opt $advanced_options.options.options
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
46 #end if
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
47 #else:
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
48 -M 0.2
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
49
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
50 #end if
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
51 ${FastaFile} >stdout.log 2> stderr.log ;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
52 echo "STDOUT CONTENT:" >> ${log} ;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
53 cat stdout.log >> ${log} ;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
54 echo "STDERR CONTENT:" >> ${log} ;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
55 cat stderr.log >> ${log} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
56 \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
57 cd tarean_output &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
58 zip -r ${ReportArchive}.zip * &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
59 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
60 cp index.html ${ReportFile} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
61 mkdir ${ReportFile.files_path} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
62 cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
63 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
64 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
65 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
66 cp *.png ${ReportFile.files_path}/ &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
67 cp *.csv ${ReportFile.files_path}/ &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
68 cp *.html ${ReportFile.files_path}/ &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
69 cp *.css ${ReportFile.files_path}/ &amp;&amp;
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
70 cp *.fasta ${ReportFile.files_path}/ 2>>$log &amp;&amp; rm -r ../tarean_output || :
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
71
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
72
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
73 </command>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
74
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
75 <inputs>
2
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
76 <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta"
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
77 help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/>
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
78
4
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
79 <conditional name="read_sampling">
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
80 <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Read sampling" help="Use this option if you want to analyze only a part of the reads" />
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
81 <when value="false">
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
82 <!-- pass -->
4
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
83 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
84 </when>
4
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
85 <when value="true">
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
86 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
3
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
87 </when>
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
88 </conditional>
67964b619af8 Uploaded
petr-novak
parents: 2
diff changeset
89
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
90 <conditional name="advanced_options">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
91 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
92 <when value="false">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
93 <!-- pass -->
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
94 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
95 <when value="true">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
96 <param name="merging" type="boolean" truevalue="0.2" falsevalue="0" checked="True" label="Perform cluster merging" help="By default, clusters connected through paired-end reads are merged"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
97 <conditional name="custom_library">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
98 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
99 <when value="false">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
100 <!-- do nothing here -->
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
101 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
102 <when value="true">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
103 <param name="library" format="fasta" type="data" label="Use custom repeat database" help="Perform additional similarity search to user-provided repeat database. The database should contain FASTA-formatted DNA sequences with headers (sequence names) in the format: '>reapeatname#class/subclass'"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
104 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
105 </conditional>
2
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
106 <param name="size_threshold" label="Cluster size threshold for detailed analysis" type="float" value="0.01" min="0.0001" max="100" help ="Minimal size (as percentage of input reads) of the smallest cluster which is analyzed; cluster with less than 20 reads are not considered."/>
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
107 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
2
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
108 <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/>
4
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
109 <conditional name="options">
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
110 <param name="options" type="select" label="Similarity search options">
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
111 <option value="ILLUMINA" selected="true">Default </option>
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
112 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
113
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
114 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
115 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
116 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
117 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
118 <!-- </option> -->
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
119 </param>
d89d4fa8a17b Uploaded
petr-novak
parents: 3
diff changeset
120 </conditional>
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
121 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
122 </conditional>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
123
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
124 <conditional name="queue_definition">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
125 <param name="queue_select" type="select" label="Select queue">
2
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
126 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
127 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
968f0867acc5 documentation and help update
petr-novak
parents: 0
diff changeset
128 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
0
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
129 </param>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
130 <when value="basic_fast_queue">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
131 <param name="queue_specification" type="text" label="Modify parameters (optional)"
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
132 value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
133 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
134
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
135 <when value="long_slow_queue">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
136 <param name="queue_specification" type="text" label="Modify parameters (optional)"
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
137 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
138 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
139 <when value="extra_long_slow_queue">
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
140 <param name="queue_specification" type="text" label="Modify parameters (optional)"
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
141 value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
142 </when>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
143 </conditional>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
144
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
145
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
146
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
147 </inputs>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
148 <outputs>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
149 <data name="log" format="txt" label="TAREAN log file"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
150 <data name="ReportArchive" format="zip" label="TAREAN Archive with HTML report from data ${FastaFile.hid}"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
151 <data name="ReportFile" format="html" label="TAREAN HTML report from data ${FastaFile.hid}"/>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
152 </outputs>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
153
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
154 <help>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
155 **HELP**
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
156
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
157 TAREAN - TAndem REpeat ANalyzer is a computational pipeline for
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
158 **unsupervised identification of satellite repeats** from unassembled
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
159 sequence reads. The pipeline uses low-pass paired-end whole genome
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
160 sequence reads and performs graph-based clustering. The resulting
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
161 clusters, representing all types of repeats present in the genome, are
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
162 then examined to identify those containing circular structures indicative
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
163 of tandem repeats. A poster summarizing TAREAN principles and
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
164 implementation can be found `here.`__
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
165
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
166
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
167 .. __: http://w3lamc.umbr.cas.cz/lamc/?page_id=312
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
168
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
169 **Input data**
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
170
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
171
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
172 The analysis requires **paired-end reads** generated by whole genome
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
173 shotgun sequencing. The data should be provided as a single input file in
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
174 fasta format with the reads interlaced (see example below). All the pairs
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
175 must be complete, i.e. both "forward" and "reverse" sequence reads must be
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
176 present. The reads should all be trimmed to the same length. The optimal
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
177 size range is between 100 and 200 nucleotides. The number of reads to be
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
178 analyzed should not exceed 1x coverage of the genome. Genome coverage
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
179 between 0.01 and 0.5x is recommended. The reads should be filtered for
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
180 quality. The recommended quality filtering is as follows: each read should
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
181 have a quality score >=10 for 95% of the bases, i.e. if your reads are 100
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
182 base pairs long, then a read only passes this quality threshold if 95
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
183 bases have a quality of 10 or higher. Additionally, any reads containing
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
184 indeterminate base pairs (indicated as N in the reads) should be removed.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
185 Finally, if either one of the reads in a pair fails to meet the
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
186 aforementioned thresholds, **both** sequences should be removed.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
187 example of interlaced input format::
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
188
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
189 >0001_f
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
190 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
191 >0001_r
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
192 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
193 >0002_f
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
194 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
195 >0002_r
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
196 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
197 >0003_f
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
198 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
199 >0003_r
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
200 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
201 ...
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
202
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
203
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
204 To perform the quality filtering on your fastQ formatted data as described
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
205 above, and to interlace your paired-end sequence reads,
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
206 please use the `Preprocessing of paired-reads`__ tool.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
207
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
208 .. __: tool_runner?tool_id=paired_fastq_filtering
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
209
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
210
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
211 **Additional parameters**
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
212
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
213 **Sample size** defines how many reads will be used during the computation.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
214 The default setting of 500,000 reads will enable detection of high copy
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
215 number satellites within several hours. For higher
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
216 sensitivity the sample size can be increased. Since the sample size affects
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
217 memory usage, this parameter may be automatically adjusted to a lower value
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
218 during the run. The maximum sample size which can be processed depends on the
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
219 repetitiveness of the analyzed genome. This significantly limits the number of reads
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
220 that can be analyzed with the TAREAN pipeline.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
221
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
222 **Perform cluster merging**. Families of repetitive elements are
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
223 frequently split into multiple clusters rather than being represented as a
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
224 single one. If you do not want to merge clusters based on the presence
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
225 of broken read pairs, disable this option.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
226
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
227 **Use custom repeat database**. This option allows users to perform similarity
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
228 comparison of identified repeats to their custom databases. The repeat class should
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
229 be encoded in FASTA headers of database entries in order to allow correct
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
230 parsing of similarity hits.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
231
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
232 **Similarity search options** By default sequence reads are compared using
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
233 mgblast program. Default threshold is explicitly set to 90% sequence
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
234 similarity spanning at least 55% of the read length (in the case of reads
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
235 differing in length it applies to the longer one). Additionally, sequence
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
236 overlap must be at least 55 nt. If you select option for shorter reads
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
237 than 100 nt, minimum overlap 55 nt is not required.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
238
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
239 By default,
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
240 mgblast search use DUST program to filter out
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
241 low-complexity sequences. If you want
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
242 to increase sensitivity of detection of satellites with shorter monomer
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
243 use option with '*no masking of low complexity repeats*'. Note that omitting
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
244 DUST filtering will significantly increase running times
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
245
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
246 **Output**
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
247
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
248 A list of clusters identified as putative satellite repeats, their genomic
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
249 abundance and various cluster characteristics are provided. Length and
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
250 consensus sequences of reconstructed monomers are also shown and
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
251 accompanied by a detailed output from kmer-based reconstruction including
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
252 sequences and sequence logos of alternative variants of monomer sequences.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
253
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
254 The output includes an **HTML summary** with a table listing all analyzed
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
255 clusters. More detailed information about clusters is provided in
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
256 additional files and directories. All results are also provided as a
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
257 downloadable **zip archive**. Since read clustering results in
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
258 thousands of clusters, the search for satellite repeats is limited to
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
259 a subset of the largest ones corresponding to the most abundant genomic
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
260 repeats. The default setting of the pipeline is to analyze all clusters containing at least
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
261 0.01% of the input reads. Besides the satellite repeats, three other
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
262 groups of clusters are reported in the output (1) LTR-retrotransposons,
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
263 (2) 45S and 5S rDNA and (3) all remaining clusters passing the size
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
264 threshold. As (1) and (2) contain sequences with circular
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
265 graphs, their consensus is calculated in the same way as for satellite
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
266 repeats. Additionally a **log file** reporting the progress of the
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
267 computational pipeline is provided.
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
268
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
269
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
270 </help>
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
271
e2b8e71b85b9 Uploaded
petr-novak
parents:
diff changeset
272 </tool>