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DSK

Description

dsk website

DSK is a k-mer counting software, similar to Jellyfish. DSK can be executed on any machine (only 1 GB memory required for a mammalian dataset) with reasonably low temporary disk usage, and supports any value of k. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.

Environment Modules

Run module spider dsk to find out what environment modules are available for this application.

Environment Variables

  • HPC_DSK_DIR - installation directory
  • HPC_DSK_BIN - executable directory
  • HPC_DSK_DOC - documentation directory
  • HPC_DSK_EXE - examples directory

Citation

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

Rizk, G., Lavenier, D., & Chikhi, R. (2013). DSK: k-mer counting with very low memory usage. Bioinformatics, 29(5), 652–653. https://doi.org/10.1093/bioinformatics/btt020

Categories

biology, ngs