Difference between revisions of "RiboPicker"
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| − | [[Category:Software]][[Category:Bioinformatics]] | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] |
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* 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] | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | + | A ''ribopicker'' alias was created for the main ribopicker.pl Perl script. To run RiboPicker use | |
| + | <code>ribopicker [options] -f <file> -dbs <list> ...</code> | ||
| + | For more information on the options run | ||
| + | ribopicker -h | ||
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{{#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.|}} | ||
Revision as of 18:57, 3 August 2012
Description
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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.
Template:App Location
Installed Versions
- 0.4.2, 0.4.3 (EL5)
- 0.4.3 (EL6)
Running the application using modules
To use ribopicker with the environment modules system at HPC the following commands are available:
Get module information for ribopicker:
$module spider ribopicker
Load the application module:
$module load ribopicker
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_RIBOPICKER_DIR - directory where ribopicker is located.
- 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
How To Run
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