Difference between revisions of "RiboPicker"

Revision as of 17:52, 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

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-<!-- ########  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 product, etc) - e.g. "http://ambermd.org/"
-Optional variables:
-INTEL - Version of the Intel Compiler e.g. "11.1"
-MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
--->
 {|
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