annotate repex_full_clustering.xml @ 15:15185fe48bf8 draft

Uploaded
author petr-novak
date Wed, 20 Dec 2023 14:24:48 +0000
parents ba67036e6b3c
children 5cca2c9aa4ad
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
15185fe48bf8 Uploaded
petr-novak
parents: 14
diff changeset
1 <tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.3" >
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;
14
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
15 export TAREAN_CPU=\$GALAXY_SLOTS;
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
16 export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB;
4
72c028e3e70e Uploaded
petr-novak
parents: 3
diff changeset
17 seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
18
349b197133dc Uploaded
petr-novak
parents:
diff changeset
19 #if $advanced_options.advanced:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
20 --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
21 --assembly_min $advanced_options.assembly_min_cluster_size
349b197133dc Uploaded
petr-novak
parents:
diff changeset
22
349b197133dc Uploaded
petr-novak
parents:
diff changeset
23 #if $advanced_options.comparative.options_comparative:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
24 --prefix_length $advanced_options.comparative.prefix_length
349b197133dc Uploaded
petr-novak
parents:
diff changeset
25 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
26
349b197133dc Uploaded
petr-novak
parents:
diff changeset
27 #if $advanced_options.custom_library.options_custom_library:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
28 -d $advanced_options.custom_library.library extra_database
349b197133dc Uploaded
petr-novak
parents:
diff changeset
29 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
30
349b197133dc Uploaded
petr-novak
parents:
diff changeset
31 #if $advanced_options.options.options:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
32 -opt $advanced_options.options.options
349b197133dc Uploaded
petr-novak
parents:
diff changeset
33 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
34 #end if
349b197133dc Uploaded
petr-novak
parents:
diff changeset
35 ${FastaFile} >stdout.log 2> stderr.log ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
36 echo "STDOUT CONTENT:" >> ${log} ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
37 cat stdout.log >> ${log} ;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
38 echo "STDERR CONTENT:" >> ${log};
349b197133dc Uploaded
petr-novak
parents:
diff changeset
39 cat stderr.log >> ${log} &amp;&amp;
4
72c028e3e70e Uploaded
petr-novak
parents: 3
diff changeset
40 /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
41 cd tarean_output &amp;&amp;
349b197133dc Uploaded
petr-novak
parents:
diff changeset
42 zip -r ${ReportArchive}.zip * &amp;&amp;
9
319156f85093 Uploaded
petr-novak
parents: 8
diff changeset
43 mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
44 cp index.html ${ReportFile} &amp;&amp;
10
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
45 mkdir -p ${ReportFile.extra_files_path} &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
46 cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
47 cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
48 cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
49 cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
50 cp *.png ${ReportFile.extra_files_path}/ &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
51 cp *.csv ${ReportFile.extra_files_path}/ &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
52 cp *.html ${ReportFile.extra_files_path}/ &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
53 cp *.css ${ReportFile.extra_files_path}/ &amp;&amp;
3c121bee9253 Uploaded
petr-novak
parents: 9
diff changeset
54 cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log &amp;&amp; rm -r ../tarean_output || :
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
55
349b197133dc Uploaded
petr-novak
parents:
diff changeset
56 </command>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
57 <inputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
58 <param name="FastaFile" label="NGS reads" type="data" format="fasta"
349b197133dc Uploaded
petr-novak
parents:
diff changeset
59 help="Input file must contain FASTA-formatted NGS reads. Illumina paired-end reads are recommended."/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
60 <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
61
349b197133dc Uploaded
petr-novak
parents:
diff changeset
62 <conditional name="read_sampling">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
63 <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
64 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
65 <!-- pass -->
15
15185fe48bf8 Uploaded
petr-novak
parents: 14
diff changeset
66 <param name="sample" label="Sample size" type="hidden" value="0" help="Number of analyzed reads"/>
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
67 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
68 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
69 <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of analyzed reads"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
70 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
71 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
72
349b197133dc Uploaded
petr-novak
parents:
diff changeset
73
349b197133dc Uploaded
petr-novak
parents:
diff changeset
74 <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
75 <option value="VIRIDIPLANTAE3.0" selected="true">Viridiplantae version 3.0 </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
76 <option value="VIRIDIPLANTAE2.2" selected="true">Viridiplantae version 2.2</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
77 <option value="METAZOA3.0" >Metazoa version 3.0</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
78 <option value="METAZOA2.0" >Metazoa version 2.0</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
79 <!-- Modify setting in config.py accordingly -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
80 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
81
349b197133dc Uploaded
petr-novak
parents:
diff changeset
82 <conditional name="advanced_options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
83 <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" />
349b197133dc Uploaded
petr-novak
parents:
diff changeset
84 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
85 <!-- pass -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
86 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
87 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
88 <conditional name="comparative">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
89 <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
90 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
91 <!-- do nothing here -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
92 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
93 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
94 <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
95 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
96 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
97
349b197133dc Uploaded
petr-novak
parents:
diff changeset
98 <conditional name="blastx">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
99 <param name="options_blastx" type="select" label="Select parameters for protein domain search">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
100 <option value="BLASTX_W2" selected="false">blastx with word size 2 (the most sensitive, slowest)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
101 <option value="BLASTX_W3" selected="true">blastx with word size 3 (default)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
102 <option value="DIAMOND" selected="false">diamond program (the least sensitive, fastest)</option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
103 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
104 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
105
349b197133dc Uploaded
petr-novak
parents:
diff changeset
106 <conditional name="options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
107 <param name="options" type="select" label="Similarity search options">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
108 <option value="ILLUMINA" selected="true">Default </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
109 <option value="ILLUMINA_DUST_OFF" selected="false">Masking of low complexity repeats disabled </option>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
110
349b197133dc Uploaded
petr-novak
parents:
diff changeset
111 <!-- <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
112 <!-- <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
113 <!-- <option value="OXFORD_NANOPORE" selected="false"> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
114 <!-- Pseudo short reads simulated from Oxford Nanopore data, experimental feature! -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
115 <!-- </option> -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
116 </param>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
117 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
118
349b197133dc Uploaded
petr-novak
parents:
diff changeset
119 <conditional name="custom_library">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
120 <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
121 <when value="false">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
122 <!-- do nothing here -->
349b197133dc Uploaded
petr-novak
parents:
diff changeset
123 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
124 <when value="true">
349b197133dc Uploaded
petr-novak
parents:
diff changeset
125 <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
126 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
127 </conditional>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
128 <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
129 <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
130 <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
131 <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
132 </when>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
133 </conditional>
14
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
134 <param name="queue_select" type="select" label="Select queue">
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
135 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
136 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
137 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
ba67036e6b3c Uploaded
petr-novak
parents: 13
diff changeset
138 </param>
2
349b197133dc Uploaded
petr-novak
parents:
diff changeset
139
349b197133dc Uploaded
petr-novak
parents:
diff changeset
140 </inputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
141 <outputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
142 <data name="log" format="txt" label="RepeatExplorer2 - log file"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
143 <data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
144 <data name="ReportFile" format="html" label="RepeatExplorer2 - HTML report from data ${FastaFile.hid}"/>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
145 </outputs>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
146
349b197133dc Uploaded
petr-novak
parents:
diff changeset
147 <help>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
148 **HELP**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
149
349b197133dc Uploaded
petr-novak
parents:
diff changeset
150 RepeatExplorer2 clustering is a computational pipeline for unsupervised
349b197133dc Uploaded
petr-novak
parents:
diff changeset
151 identification of repeats from unassembled sequence reads. The
349b197133dc Uploaded
petr-novak
parents:
diff changeset
152 pipeline uses low-pass whole genome sequence reads and performs graph-based
349b197133dc Uploaded
petr-novak
parents:
diff changeset
153 clustering. Resulting clusters, representing all types of repeats, are then
349b197133dc Uploaded
petr-novak
parents:
diff changeset
154 examined to identify and classify into repeats groups.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
155
349b197133dc Uploaded
petr-novak
parents:
diff changeset
156 **Input data**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
157
349b197133dc Uploaded
petr-novak
parents:
diff changeset
158 The analysis requires either **single** or **paired-end reads** generated
349b197133dc Uploaded
petr-novak
parents:
diff changeset
159 by whole genome shotgun sequencing provided as a single fasta-formatted file.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
160 Generally, paired-end reads provide significantly better results than single
349b197133dc Uploaded
petr-novak
parents:
diff changeset
161 reads. Reads should be of uniform length (optimal size range is 100-200 nt) and
349b197133dc Uploaded
petr-novak
parents:
diff changeset
162 the number of analyzed reads should represent less than 1x genome equivalent
349b197133dc Uploaded
petr-novak
parents:
diff changeset
163 (genome coverage of 0.01 - 0.50 x is recommended). Reads should be
349b197133dc Uploaded
petr-novak
parents:
diff changeset
164 quality-filtered (recommended filtering : quality score >=10 over 95% of bases
349b197133dc Uploaded
petr-novak
parents:
diff changeset
165 and no Ns allowed) and only **complete read pairs** should be submitted for
349b197133dc Uploaded
petr-novak
parents:
diff changeset
166 analysis. When paired reads are used, input data must be **interlaced** format
349b197133dc Uploaded
petr-novak
parents:
diff changeset
167 as fasta file:
349b197133dc Uploaded
petr-novak
parents:
diff changeset
168
349b197133dc Uploaded
petr-novak
parents:
diff changeset
169 example of interlaced input format::
349b197133dc Uploaded
petr-novak
parents:
diff changeset
170
349b197133dc Uploaded
petr-novak
parents:
diff changeset
171 >0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
172 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
173 >0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
174 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
175 >0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
176 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
177 >0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
178 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
349b197133dc Uploaded
petr-novak
parents:
diff changeset
179 >0003_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
180 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
181 >0003_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
182 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
183 ...
349b197133dc Uploaded
petr-novak
parents:
diff changeset
184
349b197133dc Uploaded
petr-novak
parents:
diff changeset
185
349b197133dc Uploaded
petr-novak
parents:
diff changeset
186 **Comparative analysis**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
187
349b197133dc Uploaded
petr-novak
parents:
diff changeset
188 For comparative analysis sequence names must contain code (prefix) for each group.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
189 Prefix in sequences names must be of fixed length.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
190
349b197133dc Uploaded
petr-novak
parents:
diff changeset
191 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
192
349b197133dc Uploaded
petr-novak
parents:
diff changeset
193 >AA0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
194 CGTAATATACATACTTGCTAGCTAGTTGGATGCATCCAACTTGCAAGCTAGTTTGATG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
195 >AA0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
196 GATTTGACGGACACACTAACTAGCTAGTTGCATCTAAGCGGGCACACTAACTAACTAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
197 >AA0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
198 ACTCATTTGGACTTAACTTTGATAATAAAAACTTAAAAAGGTTTCTGCACATGAATCG
349b197133dc Uploaded
petr-novak
parents:
diff changeset
199 >AA0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
200 TATGTTGAAAAATTGAATTTCGGGACGAAACAGCGTCTATCGTCACGACATAGTGCTC
349b197133dc Uploaded
petr-novak
parents:
diff changeset
201 >BB0001_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
202 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
203 >BB0001_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
204 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
205 >BB0002_f
349b197133dc Uploaded
petr-novak
parents:
diff changeset
206 TGACATTTGTGAACGTTAATGTTCAACAAATCTTTCCAATGTCTTTTTATCTTATCAT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
207 >BB0002_r
349b197133dc Uploaded
petr-novak
parents:
diff changeset
208 TATTGAAATACTGGACACAAATTGGAAATGAAACCTTGTGAGTTATTCAATTTATGTT
349b197133dc Uploaded
petr-novak
parents:
diff changeset
209
349b197133dc Uploaded
petr-novak
parents:
diff changeset
210
349b197133dc Uploaded
petr-novak
parents:
diff changeset
211 To prepare quality filtered and interlaced input fasta file from fastq
349b197133dc Uploaded
petr-novak
parents:
diff changeset
212 files, use `Preprocessing of paired-reads`__ tool.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
213
349b197133dc Uploaded
petr-novak
parents:
diff changeset
214 .. __: tool_runner?tool_id=paired_fastq_filtering
349b197133dc Uploaded
petr-novak
parents:
diff changeset
215
349b197133dc Uploaded
petr-novak
parents:
diff changeset
216
349b197133dc Uploaded
petr-novak
parents:
diff changeset
217 **Additional parameters**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
218
349b197133dc Uploaded
petr-novak
parents:
diff changeset
219 **Sample size** defines how many reads should be used in calculation.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
220 Default setting with 500,000 reads will enable detection of high copy
349b197133dc Uploaded
petr-novak
parents:
diff changeset
221 repeats within several hours of computation time. For higher
349b197133dc Uploaded
petr-novak
parents:
diff changeset
222 sensitivity the sample size can be set higher. Since sample size affects
349b197133dc Uploaded
petr-novak
parents:
diff changeset
223 the memory usage, this parameter may be automatically adjusted to lower
349b197133dc Uploaded
petr-novak
parents:
diff changeset
224 value during the run. Maximum sample size which can be processed depends on
349b197133dc Uploaded
petr-novak
parents:
diff changeset
225 the repetitiveness of analyzed genome.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
226
349b197133dc Uploaded
petr-novak
parents:
diff changeset
227
349b197133dc Uploaded
petr-novak
parents:
diff changeset
228 **Select taxon and protein domain database version (REXdb)**. Classification
349b197133dc Uploaded
petr-novak
parents:
diff changeset
229 of transposable elements is based on the similarity to our reference database
349b197133dc Uploaded
petr-novak
parents:
diff changeset
230 of transposable element protein domains (**REXdb**). Standalone database for Viridiplantae species
349b197133dc Uploaded
petr-novak
parents:
diff changeset
231 can be obtained on `repeatexplorer.org`__. Classification
349b197133dc Uploaded
petr-novak
parents:
diff changeset
232 system used in REXdb is described in article `Systematic survey of plant
349b197133dc Uploaded
petr-novak
parents:
diff changeset
233 LTR-retrotransposons elucidates phylogenetic relationships of their
349b197133dc Uploaded
petr-novak
parents:
diff changeset
234 polyprotein domains and provides a reference for element classification`__
349b197133dc Uploaded
petr-novak
parents:
diff changeset
235 Database for Metazoa species is still under development so use it with caution.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
236
349b197133dc Uploaded
petr-novak
parents:
diff changeset
237 .. __: http://repeatexplorer.org
349b197133dc Uploaded
petr-novak
parents:
diff changeset
238 .. __: https://doi.org/10.1186/s13100-018-0144-1
349b197133dc Uploaded
petr-novak
parents:
diff changeset
239
349b197133dc Uploaded
petr-novak
parents:
diff changeset
240 **Select parameters for protein domain search** REXdb is compared with s
349b197133dc Uploaded
petr-novak
parents:
diff changeset
241 equence clusters either using blastx or diamond aligner. Diamond program
349b197133dc Uploaded
petr-novak
parents:
diff changeset
242 is about three time faster than blastx with word size 3.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
243
349b197133dc Uploaded
petr-novak
parents:
diff changeset
244 **Similarity search options** By default sequence reads are compared using
349b197133dc Uploaded
petr-novak
parents:
diff changeset
245 mgblast program. Default threshold is explicitly set to 90% sequence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
246 similarity spanning at least 55% of the read length (in the case of reads
349b197133dc Uploaded
petr-novak
parents:
diff changeset
247 differing in length it applies to the longer one). Additionally, sequence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
248 overlap must be at least 55 nt. If you select option for shorter reads
349b197133dc Uploaded
petr-novak
parents:
diff changeset
249 than 100 nt, minimum overlap 55 nt is not required.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
250
349b197133dc Uploaded
petr-novak
parents:
diff changeset
251 By default,
349b197133dc Uploaded
petr-novak
parents:
diff changeset
252 mgblast search use DUST program to filter out
349b197133dc Uploaded
petr-novak
parents:
diff changeset
253 low-complexity sequences. If you want
349b197133dc Uploaded
petr-novak
parents:
diff changeset
254 to increase sensitivity of detection of satellites with shorter monomer
349b197133dc Uploaded
petr-novak
parents:
diff changeset
255 use option with '*no masking of low complexity repeats*'. Note that omitting
349b197133dc Uploaded
petr-novak
parents:
diff changeset
256 DUST filtering will significantly increase running times
349b197133dc Uploaded
petr-novak
parents:
diff changeset
257
349b197133dc Uploaded
petr-novak
parents:
diff changeset
258
349b197133dc Uploaded
petr-novak
parents:
diff changeset
259 **Automatic filtering of abundant satellite repeats** perform clustering on
349b197133dc Uploaded
petr-novak
parents:
diff changeset
260 smaller dataset of sequence reads to detect abundant high confidence
349b197133dc Uploaded
petr-novak
parents:
diff changeset
261 satellite repeats. If such satellites are detected, sequence reads derived
349b197133dc Uploaded
petr-novak
parents:
diff changeset
262 from these satellites are depleted from input dataset. This step enable more
349b197133dc Uploaded
petr-novak
parents:
diff changeset
263 sensitive detection of less abundant repeats as more reads can be used
349b197133dc Uploaded
petr-novak
parents:
diff changeset
264 in clustering step.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
265
349b197133dc Uploaded
petr-novak
parents:
diff changeset
266 **Use custom repeat database**. This option allows users to perform similarity
349b197133dc Uploaded
petr-novak
parents:
diff changeset
267 comparison of identified repeats to their custom databases. The repeat class must
349b197133dc Uploaded
petr-novak
parents:
diff changeset
268 be encoded in FASTA headers of database entries in order to allow correct
349b197133dc Uploaded
petr-novak
parents:
diff changeset
269 parsing of similarity hits. Required format for custom database sequence name is: ::
349b197133dc Uploaded
petr-novak
parents:
diff changeset
270
349b197133dc Uploaded
petr-novak
parents:
diff changeset
271 >reapeatname#class/subclass
349b197133dc Uploaded
petr-novak
parents:
diff changeset
272
349b197133dc Uploaded
petr-novak
parents:
diff changeset
273
349b197133dc Uploaded
petr-novak
parents:
diff changeset
274 **Output**
349b197133dc Uploaded
petr-novak
parents:
diff changeset
275
349b197133dc Uploaded
petr-novak
parents:
diff changeset
276 List of clusters identified as putative satellite repeats, their genomic
349b197133dc Uploaded
petr-novak
parents:
diff changeset
277 abundance and various cluster characteristics.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
278
349b197133dc Uploaded
petr-novak
parents:
diff changeset
279 Output includes a **HTML summary** with table listing of all analyzed
349b197133dc Uploaded
petr-novak
parents:
diff changeset
280 clusters. More detailed information about clusters is provided in
349b197133dc Uploaded
petr-novak
parents:
diff changeset
281 additional files and directories. All results are also provided as
349b197133dc Uploaded
petr-novak
parents:
diff changeset
282 downloadable **zip archive**. Additionally a **log file** reporting
349b197133dc Uploaded
petr-novak
parents:
diff changeset
283 the progress of the computational pipeline is provided.
349b197133dc Uploaded
petr-novak
parents:
diff changeset
284
349b197133dc Uploaded
petr-novak
parents:
diff changeset
285 </help>
349b197133dc Uploaded
petr-novak
parents:
diff changeset
286
349b197133dc Uploaded
petr-novak
parents:
diff changeset
287 </tool>