Difference between revisions of "CD-HIT"
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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. | 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. | ||
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Revision as of 02:41, 10 August 2012
Description
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.
Execution Environment and 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.
- HPC_CDHIT_BIN - executable directory.
- HPC_CDHIT_DOC - documentation directory.
To make the OpenMP version of CD-HIT available on EL5 load the following module:
module load cdhitmp
The EL6 version of CD-HIT has both serial and OpenMP binaries provided by the same module (see the note below).
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.