Difference between revisions of "CD-HIT"
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Revision as of 17:02, 5 July 2012
Description
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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
How To Run
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY OpenMP binaries have the same names as serial binaries, but have the "-omp" suffix added to their names.