The khmer software package: enabling efficient nucleotide sequence analysis

Creators: Crusoe, Michael R.; Skennerton, Connor T.

Abstract

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

Additional Information

© 2015 Crusoe MR et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. First published: 25 Sep 2015. khmer development has largely been supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is now funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513, as well as by the the Gordon and Betty Moore Foundation under Award number GBMF4551, all to CTB. Author contributions: CTB is the primary investigator for the khmer software package. MRC is the lead software developer from July 2013 onwards. Many significant components of khmer have their own paper describing them (see "Use Cases", above). The remaining authors each have one or more Git commits in their name. No competing interests were disclosed.

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