RiboPicker

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