annotate repex_full_clustering.xml @ 9:319156f85093 draft

Uploaded
author petr-novak
date Mon, 10 Jul 2023 10:22:18 +0000
parents 3b744b24ce50
children 3c121bee9253
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
ffe53359f758 Uploaded
petr-novak
parents: 6
diff changeset
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8" >
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
2 <stdio>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
3 <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
4 <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
5 <regex match="error" source="stderr" level="fatal" description="Unknown error" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
6 <regex match="Warning" source="stderr" level="warning" description="Unknown error" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
7 <exit_code range="1:" level="fatal" description="Error" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
8 </stdio>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
9 <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
10 <requirements>
6
4b3af335dca8 Uploaded
petr-novak
parents: 5
diff changeset
11 <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
12 </requirements>
4
72c028e3e70e Uploaded
petr-novak
parents: 3
diff changeset
13 <command>
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
14 export PYTHONHASHSEED=0;
4
72c028e3e70e Uploaded
petr-novak
parents: 3
diff changeset
15 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
16
349b197133dc Uploaded
petr-novak
parents:
diff changeset
17 #if $advanced_options.advanced:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
18 --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -D $advanced_options.blastx.options_blastx
349b197133dc Uploaded
petr-novak
parents:
diff changeset
19 --assembly_min $advanced_options.assembly_min_cluster_size
349b197133dc Uploaded
petr-novak
parents:
diff changeset
20
349b197133dc Uploaded
petr-novak
parents:
diff changeset
21 #if $advanced_options.comparative.options_comparative:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
22 --prefix_length $advanced_options.comparative.prefix_length
349b197133dc Uploaded
petr-novak
parents:
diff changeset
23 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
24
349b197133dc Uploaded
petr-novak
parents:
diff changeset
25 #if $advanced_options.custom_library.options_custom_library:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
26 -d $advanced_options.custom_library.library extra_database
349b197133dc Uploaded
petr-novak
parents:
diff changeset
27 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
28
349b197133dc Uploaded
petr-novak
parents:
diff changeset
29 #if $advanced_options.options.options:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
30 -opt $advanced_options.options.options
349b197133dc Uploaded
petr-novak
parents:
diff changeset
31 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
32 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
33 ${FastaFile} >stdout.log 2> stderr.log ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
34 echo "STDOUT CONTENT:" >> ${log} ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
35 cat stdout.log >> ${log} ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
36 echo "STDERR CONTENT:" >> ${log};
349b197133dc Uploaded
petr-novak
parents:
diff changeset
37 cat stderr.log >> ${log} &amp;&amp;
4
72c028e3e70e Uploaded
petr-novak
parents: 3
diff changeset
38 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
39 cd tarean_output &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
40 zip -r ${ReportArchive}.zip * &amp;&amp;
9
319156f85093 Uploaded
petr-novak
parents: 8
diff changeset
41 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
42 cp index.html ${ReportFile} &amp;&amp;
9
319156f85093 Uploaded
petr-novak
parents: 8
diff changeset
43 mkdir -p ${ReportFile.files_path} &amp;&amp;
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
44 cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
45 cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
46 cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
47 cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
48 cp *.png ${ReportFile.files_path}/ &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
49 cp *.csv ${ReportFile.files_path}/ &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
50 cp *.html ${ReportFile.files_path}/ &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
51 cp *.css ${ReportFile.files_path}/ &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
52 cp *.fasta ${ReportFile.files_path}/ 2>>$log &amp;&amp; rm -r ../tarean_output || :
349b197133dc Uploaded
petr-novak
parents:
diff changeset
53
349b197133dc Uploaded
petr-novak
parents:
diff changeset
54 </command>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
55 <inputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
56 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
349b197133dc Uploaded
petr-novak
parents:
diff changeset
57 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
58 <param name="paired" type="boolean" truevalue="--paired" falsevalue="" checked="True" label="Paired-end reads" help="If paired-end reads are used, left- and right-hand reads must be interlaced and all pairs must be complete. Example of the correct format is provided in the help below." />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
59
349b197133dc Uploaded
petr-novak
parents:
diff changeset
60 <conditional name="read_sampling">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
61 <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" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
62 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
63 <!-- pass -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
64 <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of analyzed reads"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
65 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
66 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
67 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
68 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
69 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
70
349b197133dc Uploaded
petr-novak
parents:
diff changeset
71
349b197133dc Uploaded
petr-novak
parents:
diff changeset
72 <param name="taxon" label="Select taxon and protein domain database version (REXdb)" type="select" help="Reference database of transposable element protein domains - REXdb - is used for annotation of repeats">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
73 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
74 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
75 <option value="METAZOA3.0" >Metazoa version 3.0</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
76 <option value="METAZOA2.0" >Metazoa version 2.0</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
77 <!-- Modify setting in config.py accordingly -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
78 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
79
349b197133dc Uploaded
petr-novak
parents:
diff changeset
80 <conditional name="advanced_options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
81 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
82 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
83 <!-- pass -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
84 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
85 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
86 <conditional name="comparative">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
87 <param name="options_comparative" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Perform comparative analysis" help="Use this options to analyze multiple samples simultaneously"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
88 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
89 <!-- do nothing here -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
90 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
91 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
92 <param name="prefix_length" label="Group code length" type="integer" value="3" min="1" max="10" help="For comparative analysis, reads from different samples are distinguished by sample codes included as prefix to the read names. See example below."/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
93 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
94 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
95
349b197133dc Uploaded
petr-novak
parents:
diff changeset
96 <conditional name="blastx">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
97 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
98 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
99 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
100 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
101 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
102 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
103
349b197133dc Uploaded
petr-novak
parents:
diff changeset
104 <conditional name="options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
105 <param name="options" type="select" label="Similarity search options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
106 <option value="ILLUMINA" selected="true">Default </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
107 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
108
349b197133dc Uploaded
petr-novak
parents:
diff changeset
109 <!-- <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">Illumina reads, sensitive search (search parameters: mgblast, min PID 80, -W8) slow, experimental feature!</option> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
110 <!-- <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">Illumina reads, more sensitive search (search parameters: blastn, min PID 80, -W6) extremely slow, experimental feature!</option> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
111 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
112 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
113 <!-- </option> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
114 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
115 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
116
349b197133dc Uploaded
petr-novak
parents:
diff changeset
117 <conditional name="custom_library">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
118 <param name="options_custom_library" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use custom repeat database"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
119 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
120 <!-- do nothing here -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
121 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
122 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
123 <param name="library" format="fasta" type="data" label="Custom repeat database" help="The database should contain DNA sequences in FASTA format. The required format for sequence IDs is : '>reapeatname#class/subclass'"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
124 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
125 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
126 <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; clusters with less than 20 reads are not considered."/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
127 <param name="automatic_filtering" label="Perform automatic filtering of abundant satellite repeats" help="Automatic filtering identifies the most abundant tandem repeats and partially removes their reads from the analysis. This enables to analyze higher proportions of other less abundant repeats." type="boolean" truevalue="--automatic_filtering" falsevalue="" checked="false"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
128 <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 to keep original names."/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
129 <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
130 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
131 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
132
5
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
133 <conditional name="queue_definition">
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
134 <param name="queue_select" type="select" label="Select queue">
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
138 </param>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
139 <when value="basic_fast_queue">
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
140 <param name="queue_specification" type="text" label="Modify parameters (optional)"
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
141 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" />
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
142 </when>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
143
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
144 <when value="long_slow_queue">
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
145 <param name="queue_specification" type="text" label="Modify parameters (optional)"
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
146 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" />
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
147 </when>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
148 <when value="extra_long_slow_queue">
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
149 <param name="queue_specification" type="text" label="Modify parameters (optional)"
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
150 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" />
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
151 </when>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
152 </conditional>
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
153
397394c00bf7 Uploaded
petr-novak
parents: 4
diff changeset
154
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
155
349b197133dc Uploaded
petr-novak
parents:
diff changeset
156 </inputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
157 <outputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
158 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
159 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
160 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
161 </outputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
162
349b197133dc Uploaded
petr-novak
parents:
diff changeset
163 <help>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
164 **HELP**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
165
349b197133dc Uploaded
petr-novak
parents:
diff changeset
166 RepeatExplorer2 clustering is a computational pipeline for unsupervised
349b197133dc Uploaded
petr-novak
parents:
diff changeset
167 identification of repeats from unassembled sequence reads. The
349b197133dc Uploaded
petr-novak
parents:
diff changeset
168 pipeline uses low-pass whole genome sequence reads and performs graph-based
349b197133dc Uploaded
petr-novak
parents:
diff changeset
169 clustering. Resulting clusters, representing all types of repeats, are then
349b197133dc Uploaded
petr-novak
parents:
diff changeset
170 examined to identify and classify into repeats groups.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
171
349b197133dc Uploaded
petr-novak
parents:
diff changeset
172 **Input data**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
173
349b197133dc Uploaded
petr-novak
parents:
diff changeset
174 The analysis requires either **single** or **paired-end reads** generated
349b197133dc Uploaded
petr-novak
parents:
diff changeset
175 by whole genome shotgun sequencing provided as a single fasta-formatted file.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
176 Generally, paired-end reads provide significantly better results than single
349b197133dc Uploaded
petr-novak
parents:
diff changeset
177 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
349b197133dc Uploaded
petr-novak
parents:
diff changeset
178 the number of analyzed reads should represent less than 1x genome equivalent
349b197133dc Uploaded
petr-novak
parents:
diff changeset
179 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
349b197133dc Uploaded
petr-novak
parents:
diff changeset
180 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
349b197133dc Uploaded
petr-novak
parents:
diff changeset
181 and no Ns allowed) and only **complete read pairs** should be submitted for
349b197133dc Uploaded
petr-novak
parents:
diff changeset
182 analysis. When paired reads are used, input data must be **interlaced** format
349b197133dc Uploaded
petr-novak
parents:
diff changeset
183 as fasta file:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
184
349b197133dc Uploaded
petr-novak
parents:
diff changeset
185 example of interlaced input format::
349b197133dc Uploaded
petr-novak
parents:
diff changeset
186
349b197133dc Uploaded
petr-novak
parents:
diff changeset
187 >0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
188 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
189 >0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
190 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
191 >0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
192 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
193 >0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
194 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
349b197133dc Uploaded
petr-novak
parents:
diff changeset
195 >0003_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
196 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
197 >0003_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
198 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
199 ...
349b197133dc Uploaded
petr-novak
parents:
diff changeset
200
349b197133dc Uploaded
petr-novak
parents:
diff changeset
201
349b197133dc Uploaded
petr-novak
parents:
diff changeset
202 **Comparative analysis**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
203
349b197133dc Uploaded
petr-novak
parents:
diff changeset
204 For comparative analysis sequence names must contain code (prefix) for each group.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
205 Prefix in sequences names must be of fixed length.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
206
349b197133dc Uploaded
petr-novak
parents:
diff changeset
207 Example of labeling two groups with where **group code length** is 2 and is used to distinguish groups - AA and BB ::
349b197133dc Uploaded
petr-novak
parents:
diff changeset
208
349b197133dc Uploaded
petr-novak
parents:
diff changeset
209 >AA0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
210 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
211 >AA0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
212 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
213 >AA0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
214 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
215 >AA0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
216 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
349b197133dc Uploaded
petr-novak
parents:
diff changeset
217 >BB0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
218 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
219 >BB0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
220 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
221 >BB0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
222 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
223 >BB0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
224 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
225
349b197133dc Uploaded
petr-novak
parents:
diff changeset
226
349b197133dc Uploaded
petr-novak
parents:
diff changeset
227 To prepare quality filtered and interlaced input fasta file from fastq
349b197133dc Uploaded
petr-novak
parents:
diff changeset
228 files, use `Preprocessing of paired-reads`__ tool.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
229
349b197133dc Uploaded
petr-novak
parents:
diff changeset
230 .. __: tool_runner?tool_id=paired_fastq_filtering
349b197133dc Uploaded
petr-novak
parents:
diff changeset
231
349b197133dc Uploaded
petr-novak
parents:
diff changeset
232
349b197133dc Uploaded
petr-novak
parents:
diff changeset
233 **Additional parameters**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
234
349b197133dc Uploaded
petr-novak
parents:
diff changeset
235 **Sample size** defines how many reads should be used in calculation.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
236 Default setting with 500,000 reads will enable detection of high copy
349b197133dc Uploaded
petr-novak
parents:
diff changeset
237 repeats within several hours of computation time. For higher
349b197133dc Uploaded
petr-novak
parents:
diff changeset
238 sensitivity the sample size can be set higher. Since sample size affects
349b197133dc Uploaded
petr-novak
parents:
diff changeset
239 the memory usage, this parameter may be automatically adjusted to lower
349b197133dc Uploaded
petr-novak
parents:
diff changeset
240 value during the run. Maximum sample size which can be processed depends on
349b197133dc Uploaded
petr-novak
parents:
diff changeset
241 the repetitiveness of analyzed genome.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
242
349b197133dc Uploaded
petr-novak
parents:
diff changeset
243
349b197133dc Uploaded
petr-novak
parents:
diff changeset
244 **Select taxon and protein domain database version (REXdb)**. Classification
349b197133dc Uploaded
petr-novak
parents:
diff changeset
245 of transposable elements is based on the similarity to our reference database
349b197133dc Uploaded
petr-novak
parents:
diff changeset
246 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
349b197133dc Uploaded
petr-novak
parents:
diff changeset
247 can be obtained on `repeatexplorer.org`__. Classification
349b197133dc Uploaded
petr-novak
parents:
diff changeset
248 system used in REXdb is described in article `Systematic survey of plant
349b197133dc Uploaded
petr-novak
parents:
diff changeset
249 LTR-retrotransposons elucidates phylogenetic relationships of their
349b197133dc Uploaded
petr-novak
parents:
diff changeset
250 polyprotein domains and provides a reference for element classification`__
349b197133dc Uploaded
petr-novak
parents:
diff changeset
251 Database for Metazoa species is still under development so use it with caution.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
252
349b197133dc Uploaded
petr-novak
parents:
diff changeset
253 .. __: http://repeatexplorer.org
349b197133dc Uploaded
petr-novak
parents:
diff changeset
254 .. __: https://doi.org/10.1186/s13100-018-0144-1
349b197133dc Uploaded
petr-novak
parents:
diff changeset
255
349b197133dc Uploaded
petr-novak
parents:
diff changeset
256 **Select parameters for protein domain search** REXdb is compared with s
349b197133dc Uploaded
petr-novak
parents:
diff changeset
257 equence clusters either using blastx or diamond aligner. Diamond program
349b197133dc Uploaded
petr-novak
parents:
diff changeset
258 is about three time faster than blastx with word size 3.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
259
349b197133dc Uploaded
petr-novak
parents:
diff changeset
260 **Similarity search options** By default sequence reads are compared using
349b197133dc Uploaded
petr-novak
parents:
diff changeset
261 mgblast program. Default threshold is explicitly set to 90% sequence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
262 similarity spanning at least 55% of the read length (in the case of reads
349b197133dc Uploaded
petr-novak
parents:
diff changeset
263 differing in length it applies to the longer one). Additionally, sequence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
264 overlap must be at least 55 nt. If you select option for shorter reads
349b197133dc Uploaded
petr-novak
parents:
diff changeset
265 than 100 nt, minimum overlap 55 nt is not required.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
266
349b197133dc Uploaded
petr-novak
parents:
diff changeset
267 By default,
349b197133dc Uploaded
petr-novak
parents:
diff changeset
268 mgblast search use DUST program to filter out
349b197133dc Uploaded
petr-novak
parents:
diff changeset
269 low-complexity sequences. If you want
349b197133dc Uploaded
petr-novak
parents:
diff changeset
270 to increase sensitivity of detection of satellites with shorter monomer
349b197133dc Uploaded
petr-novak
parents:
diff changeset
271 use option with '*no masking of low complexity repeats*'. Note that omitting
349b197133dc Uploaded
petr-novak
parents:
diff changeset
272 DUST filtering will significantly increase running times
349b197133dc Uploaded
petr-novak
parents:
diff changeset
273
349b197133dc Uploaded
petr-novak
parents:
diff changeset
274
349b197133dc Uploaded
petr-novak
parents:
diff changeset
275 **Automatic filtering of abundant satellite repeats** perform clustering on
349b197133dc Uploaded
petr-novak
parents:
diff changeset
276 smaller dataset of sequence reads to detect abundant high confidence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
277 satellite repeats. If such satellites are detected, sequence reads derived
349b197133dc Uploaded
petr-novak
parents:
diff changeset
278 from these satellites are depleted from input dataset. This step enable more
349b197133dc Uploaded
petr-novak
parents:
diff changeset
279 sensitive detection of less abundant repeats as more reads can be used
349b197133dc Uploaded
petr-novak
parents:
diff changeset
280 in clustering step.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
281
349b197133dc Uploaded
petr-novak
parents:
diff changeset
282 **Use custom repeat database**. This option allows users to perform similarity
349b197133dc Uploaded
petr-novak
parents:
diff changeset
283 comparison of identified repeats to their custom databases. The repeat class must
349b197133dc Uploaded
petr-novak
parents:
diff changeset
284 be encoded in FASTA headers of database entries in order to allow correct
349b197133dc Uploaded
petr-novak
parents:
diff changeset
285 parsing of similarity hits. Required format for custom database sequence name is: ::
349b197133dc Uploaded
petr-novak
parents:
diff changeset
286
349b197133dc Uploaded
petr-novak
parents:
diff changeset
287 >reapeatname#class/subclass
349b197133dc Uploaded
petr-novak
parents:
diff changeset
288
349b197133dc Uploaded
petr-novak
parents:
diff changeset
289
349b197133dc Uploaded
petr-novak
parents:
diff changeset
290 **Output**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
291
349b197133dc Uploaded
petr-novak
parents:
diff changeset
292 List of clusters identified as putative satellite repeats, their genomic
349b197133dc Uploaded
petr-novak
parents:
diff changeset
293 abundance and various cluster characteristics.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
294
349b197133dc Uploaded
petr-novak
parents:
diff changeset
295 Output includes a **HTML summary** with table listing of all analyzed
349b197133dc Uploaded
petr-novak
parents:
diff changeset
296 clusters. More detailed information about clusters is provided in
349b197133dc Uploaded
petr-novak
parents:
diff changeset
297 additional files and directories. All results are also provided as
349b197133dc Uploaded
petr-novak
parents:
diff changeset
298 downloadable **zip archive**. Additionally a **log file** reporting
349b197133dc Uploaded
petr-novak
parents:
diff changeset
299 the progress of the computational pipeline is provided.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
300
349b197133dc Uploaded
petr-novak
parents:
diff changeset
301 </help>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
302
349b197133dc Uploaded
petr-novak
parents:
diff changeset
303 </tool>