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Gerbil

Description

gerbil website

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.

Environment 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:

Erbert, M., Rechner, S., & Müller-Hannemann, M. (2017). Gerbil: A fast and memory-efficient k-mer counter with GPU-support. Algorithms for Molecular Biology, 12, 9. https://doi.org/10.1186/s13015-017-0097-9

Categories

phylogenetics