riboPicker

Search Software

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.

SW Documentation: 

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

Homepage:http://ribopicker.sourceforge.net/manual.html

 

Short Name: 
ribopicker
SW Module: 
ribopicker
Service Level: 
Minimal
SW Category: