RiboPicker: Difference between revisions
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__NOTOC__ __NOEDITSECTION__ | __NOTOC__ __NOEDITSECTION__ | ||
[[Category:Software]][[Category: | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] | ||
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|ribopicker}} | |{{#vardefine:app|ribopicker}} | ||
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|{{#vardefine:policy|}} <!--Enable policy section --> | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
|{{#vardefine:faq| | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
|{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
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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. | 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. | ||
<!--Modules--> | <!--Modules--> | ||
== | ==Environment Modules== | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_RIBOPICKER_BIN - executable directory | * HPC_RIBOPICKER_BIN - executable directory | ||
<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}| | {{#if: {{#var: exe}}| | ||
==Databases== | ==Databases== | ||
The following Ribosomal RNA databases are available for use with RiboPicker at HPC: | The following Ribosomal RNA databases are available for use with RiboPicker at HPC: | ||
Latest revision as of 21:50, 21 August 2022
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.
Environment Modules
Run module spider ribopicker to find out what environment modules are available for this application.
System Variables
- HPC_RIBOPICKER_DIR - installation directory
- 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
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