Difference between revisions of "CD-HIT"
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{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|cdhit}} | |{{#vardefine:app|cdhit}} | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * 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. | ||
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WRITE CITATION HERE | WRITE CITATION HERE | ||
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Latest revision as of 18:24, 12 August 2022
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.
Environment Modules
Run module spider cdhit to find out what environment modules are available for this application.
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.