Difference between revisions of "CD-HIT"
Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 2: | Line 2: | ||
__NOEDITSECTION__ | __NOEDITSECTION__ | ||
[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | ||
| − | + | {|<!--Main settings - REQUIRED--> | |
| − | {| | ||
| − | <!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|cdhit}} | |{{#vardefine:app|cdhit}} | ||
|{{#vardefine:url|http://weizhong-lab.ucsd.edu/cd-hit/}} | |{{#vardefine:url|http://weizhong-lab.ucsd.edu/cd-hit/}} | ||
| − | |||
| − | |||
| − | |||
|{{#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--> | ||
| Line 30: | Line 25: | ||
===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| + | ==System Variables== | ||
| + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_CDHIT_BIN - executable directory. | * HPC_CDHIT_BIN - executable directory. | ||
* HPC_CDHIT_DOC - documentation directory. | * HPC_CDHIT_DOC - documentation directory. | ||
| − | + | <!--Additional--> | |
| − | + | {{#if: {{#var: exe}}|==Additional Information== | |
| − | |||
| − | {{#if: {{#var: exe}}|== | ||
| − | |||
OpenMP binaries have the same names as serial binaries, but have the "-omp" suffix added to their names. | OpenMP binaries have the same names as serial binaries, but have the "-omp" suffix added to their names. | ||
| + | }} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| Line 52: | Line 47: | ||
WRITE CITATION HERE | WRITE CITATION HERE | ||
|}} | |}} | ||
| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:11, 6 December 2019
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
System Variables
- HPC_CDHIT_DIR - installation directory
- HPC_CDHIT_BIN - executable directory.
- HPC_CDHIT_DOC - documentation directory.
Additional Information
OpenMP binaries have the same names as serial binaries, but have the "-omp" suffix added to their names.
Validation
- Validated 4/5/2018