Difference between revisions of "CD-HIT"
Moskalenko (talk | contribs) (Created page with "__NOTOC__ __NOEDITSECTION__ Category:SoftwareCategory:BioinformaticsCategory:Genomics <!-- ######## Template Configuration ######## --> <!--Edit definitions of the v...") |
Moskalenko (talk | contribs) |
||
| Line 36: | Line 36: | ||
{{App_Location|app={{#var:app}}|{{#var:ver}}}} | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
==Available versions== | ==Available versions== | ||
| − | * 4.5.7 (serial and | + | * 4.5.7 (serial and openmp). |
<!-- --> | <!-- --> | ||
{{#if: {{#var: mod}}|==Running the application using modules== | {{#if: {{#var: mod}}|==Running the application using modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| − | To make the | + | To make the OpenMP version of CD-HIT available load the following modules: |
| − | module load | + | module load cdhitmp |
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
Revision as of 23:15, 30 January 2012
Description
{{{name}}} website
CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.
Template:App Location
Available versions
- 4.5.7 (serial and openmp).
Running the application using modules
To use cdhit with the environment modules system at HPC the following commands are available:
Get module information for cd-hit:
$module spider cdhit
Load the default application module:
$module load cdhit
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_CDHIT_DIR - directory where cdhit is located.
To make the OpenMP version of CD-HIT available load the following modules:
module load cdhitmp