Difference between revisions of "CD-HIT"
Moskalenko (talk | contribs) m (Text replace - "<!-- ######## Template Configuration ######## --> <!--Edit definitions of the variables used in template calls Required variables: app - lowercase name of the application e.g. "amber" url - url of the software page (project, company prod) |
Moskalenko (talk | contribs) m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "") |
||
| Line 10: | Line 10: | ||
|{{#vardefine:intel|}} <!-- E.g. "11.1" --> | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | ||
| − | + | ||
| − | |||
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|1}} <!--Present manual instructions for running the software --> | ||
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
Revision as of 17:52, 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.
Required Modules
Serial
- 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.