The khmer software package: enabling efficient nucleotide sequence analysis

Date
2015-09-25
Authors
Crusoe, Michael
Alameldin, Hussein
Awad, Sherine
Howe, Adina
Boucher, Elmar
Caldwell, Adam
Cartwright, Reed
Charbonneau, Amanda
Constantinides, Bede
Edvenson, Greg
Fay, Scott
Fenton, Jacob
Fenzl, Thomas
Fish, Jordan
Garcia-Gutierrez, Leonor
Garland, Phillip
Gluck, Jonathan
González, Iván
Guermond, Sarah
Guo, Jiarong
Gupta, Aditi
Herr, Joshua
Howe, Adina
Hyer, Alex
Härpfer, Andreas
Irber, Luiz
Kidd, Rhys
Lin, David
Lippi, Justin
Mansour, Tamer
McA'Nulty, Pamela
McDonald, Erin
Mizzi, Jessica
Murray, Kevin
Nahum, Joshua
Nanlohy, Kaben
Nederbragt, Alexander
Ortiz-Zuazaga, Humberto
Ory, Jeramia
Pell, Jason
Pepe-Ranney, Charles
Russ, Zachary
Schwarz, Erich
Scott, Camille
Seaman, Josiah
Sievert, Scott
Simpson, Jared
Skennerton, Connor
Spencer, James
Srinivasan, Ramakrishnan
Standage, Daniel
Stapleton, James
Steinman, Susan
Stein, Joe
Taylor, Benjamin
Tremble, Will
Wiencko, Heather
Wright, Michael
Wyss, Brian
Zhang, Qingpeng
zyme, en
Brown, C. Titus
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Howe, Adina
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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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