Difference between revisions of "Gerbil"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|gerbil}} |{{#vardefine:url|https://github.com/uni-halle/gerbil}} <!--CONFIGU...") |
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | |||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 14:34, 3 January 2020
Description
A basic task in bioinformatics is the counting of k-mers in genome strings. The k-mer counting problem is to build a histogram of all substrings of length k in a given genome sequence. Gerbil is a k-mer counter that is specialized for high effiency when counting k-mers for large k. The software is decribed here.
Environment Modules
Run module spider gerbil to find out what environment modules are available for this application.
System Variables
- HPC_GERBIL_DIR - installation directory
- HPC_GERBIL_BIN - executable directory
Citation
If you publish research that uses gerbil you have to cite it as follows: