ribopicker
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.
Info
Module Name
ribopicker
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
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
Agate Modules
Default
0.4.3
Other Modules
0.4.3
Mangi Modules
Default
0.4.3
Other Modules
0.4.3
Mesabi Modules
Default
0.4.3
Other Modules
0.4.3