ribopicker

Summary

• Module Name: ribopicker

• Support Level: Secondary Support

• Software Access Level: Open Access

• Home Page: http://ribopicker.sourceforge.net/manual.html

Software Description

The riboPicker tool can be used to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. At MSI, we provide a stand-alone version of the tool.  So the user must have some linux background to use this tool. If you are not familiar with the command line, the developer also provides a web-version of the software at: http://edwards.sdsu.edu/cgi-bin/ribopicker/ribopicker.cgi Please note, for the web-version, your input file should be less than 2GB in size.

General Linux

To run this software interactively in a Linux environment run the commands:

module load ribopicker
ribopicker -h

or

ribopicker [options] -f <file> -dbs <list> ...

Since ribopicker will search ribosomal sequences in known databases, please use:

ribopicker -show_dbs

to check for available databases at MSI.

ribopicker -f input.fasta -dbs slr,ssr