The khmer software package: enabling efficient nucleotide sequence analysis
Date
2015-09-25
Authors
Crusoe, Michael
Alameldin, Hussein
Awad, Sherine
Boucher, Elmar
Caldwell, Adam
Cartwright, Reed
Charbonneau, Amanda
Constantinides, Bede
Edvenson, Greg
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Bioinformatics and Computational BiologyAgricultural and Biosystems Engineering
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/.
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This article is from F1000Research 2015, 4:900 (doi:10.12688/f1000research.6924.1). Posted with permission.
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Thu Jan 01 00:00:00 UTC 2015