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The khmer software package: enabling efficient nucleotide sequence analysis.

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/.

SUBMITTER: Crusoe MR 

PROVIDER: S-EPMC4608353 | biostudies-other | 2015

REPOSITORIES: biostudies-other

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The khmer software package: enabling efficient nucleotide sequence analysis.

Crusoe Michael R MR   Alameldin Hussien F HF   Awad Sherine S   Boucher Elmar E   Caldwell Adam A   Cartwright Reed R   Charbonneau Amanda A   Constantinides Bede B   Edvenson Greg G   Fay Scott S   Fenton Jacob J   Fenzl Thomas T   Fish Jordan J   Garcia-Gutierrez Leonor L   Garland Phillip P   Gluck Jonathan J   González Iván I   Guermond Sarah S   Guo Jiarong J   Gupta Aditi A   Herr Joshua R JR   Howe Adina A   Hyer Alex A   Härpfer Andreas A   Irber Luiz L   Kidd Rhys R   Lin David D   Lippi Justin J   Mansour Tamer T   McA'Nulty Pamela P   McDonald Eric E   Mizzi Jessica J   Murray Kevin D KD   Nahum Joshua R JR   Nanlohy Kaben K   Nederbragt Alexander Johan AJ   Ortiz-Zuazaga Humberto H   Ory Jeramia J   Pell Jason J   Pepe-Ranney Charles C   Russ Zachary N ZN   Schwarz Erich E   Scott Camille C   Seaman Josiah J   Sievert Scott S   Simpson Jared J   Skennerton Connor T CT   Spencer James J   Srinivasan Ramakrishnan R   Standage Daniel D   Stapleton James A JA   Steinman Susan R SR   Stein Joe J   Taylor Benjamin B   Trimble Will W   Wiencko Heather L HL   Wright Michael M   Wyss Brian B   Zhang Qingpeng Q   Zyme En E   Brown C Titus CT  

F1000Research 20150925

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/. ...[more]

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