Published in
F1000Research, F1000Research, (4), p. 900, 2015
DOI: 10.12688/f1000research.6924.1
Links
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- [www.researchgate.net] | PDF
- [www.ncbi.nlm.nih.gov] | PDF
- [europepmc.org] | PDF
- [authors.library.caltech.edu] | PDF
Tools
The khmer software package: enabling efficient nucleotide sequence analysis
Journal article published in 2015 by
Andreas Harpfer,
Michael R. Crusoe 
,
Hussien F. Alameldin,
Sherine Awad,
Elmar Boucher,
Jacob Fenton,
Adam Caldwell,
Thomas Fenzl,
Reed Cartwright,
Jordan Fish,
Amanda Charbonneau,
Leonor Garcia-Gutierrez,
Phillip Garland,
Bede Constantinides ,
Jonathan Gluck
and other authors.
,
Hussien F. Alameldin,
Sherine Awad,
Elmar Boucher,
Jacob Fenton,
Adam Caldwell,
Thomas Fenzl,
Reed Cartwright,
Jordan Fish,
Amanda Charbonneau,
Leonor Garcia-Gutierrez,
Phillip Garland,
Bede Constantinides ,
Jonathan Gluck
and other authors.
This paper is made freely available by the publisher.
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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/.