Difference between revisions of "CD-HIT"

Jump to navigation Jump to search
m (Text replace - "Usage policy" to "Usage Policy")
m (Text replace - "{{#if: {{#var: mod}}|==Execution Environment and Modules== {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}" to "==Required Modules== modules documentation ===Serial=== *{{#var:app}}")
Line 36: Line 36:
{{#if: {{#var: mod}}|==Execution Environment and Modules==
==Required Modules==
[[Modules|modules documentation]]
* HPC_CDHIT_BIN - executable directory.
* HPC_CDHIT_BIN - executable directory.
* HPC_CDHIT_DOC - documentation directory.
* HPC_CDHIT_DOC - documentation directory.

Revision as of 16:55, 10 August 2012


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.

Required Modules

modules documentation


  • cdhit
  • 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.