Revision as of 02:02, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
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cdhit 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.

Available versions

  • 4.5.7 (serial and openmp).

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.