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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 openmpi).

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 MPI version of CD-HIT available load the following modules:

module load intel/10.1 openmpi cdhit