Difference between revisions of "RiboPicker"
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Moskalenko (talk | contribs) m (Text replace - "<!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in template calls Required variables: app - lowercase name of the application e.g. "amber" url - url of the software page (project, company prod) |
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− | __NOTOC__ | + | __NOTOC__ __NOEDITSECTION__ |
− | __NOEDITSECTION__ | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
− | [[Category:Software]][[Category: | + | {|<!--Main settings - REQUIRED--> |
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− | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|ribopicker}} | |{{#vardefine:app|ribopicker}} | ||
|{{#vardefine:url|http://ribopicker.sourceforge.net/}} | |{{#vardefine:url|http://ribopicker.sourceforge.net/}} | ||
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|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
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The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. | The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. | ||
− | + | <!--Modules--> | |
− | + | ==Environment Modules== | |
− | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
− | + | ==System Variables== | |
− | <!-- --> | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
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− | * HPC_{{uc:{{#var:app}}}}_DIR - directory | ||
* HPC_RIBOPICKER_BIN - executable directory | * HPC_RIBOPICKER_BIN - executable directory | ||
− | + | <!--Additional--> | |
+ | {{#if: {{#var: exe}}| | ||
==Databases== | ==Databases== | ||
The following Ribosomal RNA databases are available for use with RiboPicker at HPC: | The following Ribosomal RNA databases are available for use with RiboPicker at HPC: | ||
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* ssr - Small Subunit RNA database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz] | * ssr - Small Subunit RNA database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz] | ||
* lsr - Large Subunit non-redundant truncated database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ LSURef_108_tax_silva_trunc.fasta.tgz] | * lsr - Large Subunit non-redundant truncated database from the SILVA project [http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/ LSURef_108_tax_silva_trunc.fasta.tgz] | ||
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A ''ribopicker'' alias was created for the main ribopicker.pl Perl script. To run RiboPicker use | A ''ribopicker'' alias was created for the main ribopicker.pl Perl script. To run RiboPicker use | ||
<code>ribopicker [options] -f <file> -dbs <list> ...</code> | <code>ribopicker [options] -f <file> -dbs <list> ...</code> | ||
For more information on the options run | For more information on the options run | ||
ribopicker -h | ribopicker -h | ||
− | + | }} | |
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} |
Latest revision as of 21:50, 21 August 2022
Description
The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
Environment Modules
Run module spider ribopicker
to find out what environment modules are available for this application.
System Variables
- HPC_RIBOPICKER_DIR - installation directory
- HPC_RIBOPICKER_BIN - executable directory
Databases
The following Ribosomal RNA databases are available for use with RiboPicker at HPC:
- rrnadb - Non-redundant Ribosomal RNA database from rrnadb.
- ssr - Small Subunit RNA database from the SILVA project SSURef_108_NR_tax_silva_trunc_v2.fasta.tgz
- lsr - Large Subunit non-redundant truncated database from the SILVA project LSURef_108_tax_silva_trunc.fasta.tgz
A ribopicker alias was created for the main ribopicker.pl Perl script. To run RiboPicker use
ribopicker [options] -f <file> -dbs <list> ...
For more information on the options run
ribopicker -h