Difference between revisions of "RiboPicker"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "") |
Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
||
| Line 8: | Line 8: | ||
|{{#vardefine:url|http://ribopicker.sourceforge.net/}} | |{{#vardefine:url|http://ribopicker.sourceforge.net/}} | ||
<!--Compiler and MPI settings - OPTIONAL --> | <!--Compiler and MPI settings - OPTIONAL --> | ||
| − | + | ||
| − | |||
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
Revision as of 17:53, 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)
- 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