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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.

System Variables

  • HPC_GERBIL_DIR - installation directory
  • HPC_GERBIL_BIN - executable directory


If you publish research that uses gerbil you have to cite it as follows:

Marius Erbert, Steffen Rechner, and Matthias Müller-Hannemann, Gerbil: A fast and memory-efficient k-mer counter with GPU-support, Algorithms for Molecular Biology (2017) 12:9, open access.