Difference between revisions of "RiboPicker"

Revision as of 02:03, 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

@@ Line 39: / Line 39: @@
 * 0.4.3 (EL6)
 <!-- -->
-{{#if: {{#var: mod}}|==Running the application using modules==
+{{#if: {{#var: mod}}|==Execution Environment and Modules==
 To use {{#var:app}} with the environment modules system at HPC the following commands are available: