Difference between revisions of "RiboPicker"
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Revision as of 16:33, 10 August 2012
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.
Installed Versions
- 0.4.2, 0.4.3 (EL5)
- 0.4.3 (EL6)
Execution Environment and 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