Commit 28bc48f4 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add blast_contamination_search documentation

parent 7db07933
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
......
[interface]
classification = sequencing
classification = sequence / cleaning
[parameters]
; blast parameters
$;EXPECT$; = 1e-5
$;FILTER$; = F
$;FILTER$; = [ F|T ]
$;DATABASE_MATCHES$; = 150
$;DESCRIPTIONS$; = 150
$;OTHER_OPTS$; =
......
<p>
This script search contamination from a fasta file against blast bank
Search contamination using blast against databases. Calls blastall and a blast_filter to detect contaminant sequences.
</p>
<h3>input</h3>
<h3>inputs</h3>
<p>
This component calls :
- blastall command on the list of input databank
- the perl script blast_filter.pl which take output blast and file along pci and pcq to generate m9 blast file
Component allows these types of input:
</p>
<ul>
<li>blast e-value,</li>
<li>blast filter,</li>
<li>blast nb database matches,</li>
<li>blast nb descriptions,</li>
<li>blast nb descriptions,</li>
<li>blast output format,</li>
<li>pci filter : percent of identity query,</li>
<li>pcq filter : percent of query length,</li>
<li>bank path : path to a bank</li>
<li>sequences files : one or more sequence file
<li>input file: This program accepts fasta files as input.</li>
<li>databases: the list of path to the formated database separated by a coma (database shouldnt have a "." in there name).</li>
<li>ng6cfg file: The NG6 run config file the analyse belongs to.</li>
<li>project id: The NG6 project id the analyse belongs to.</li>
</ul>
<h3>output</h3>
</p>
<h3>outputs</h3>
<p>
Generate a contamination file list.
</p>
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Outputs a name file with all sequences id detected as contaminant and the blast m8 file.
</p>
<h3>parameters</h3>
<p>
<ul>
<li>expect: The blast e-value,</li>
<li>filter: Filter low complex region if set at T,</li>
<li>database matches: Blast number of databases matches,</li>
<li>descriptions: Blast number of descriptions,</li>
<li>other opts: Options to pass to blastall command,</li>
<li>pci: Min identity percent to consider the hit as contamination,</li>
<li>pcq: Min hit length percent to consider it as contamination,</li>
<li>analyse name: The analyse name to display in ng6,</li>
<li>analyse description: The analyse description to display in ng6,</li>
<li>results archive name: The results archive name to display in ng6.</li>
</ul>
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