The khmer software package: enabling efficient nucleotide sequence analysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Crusoe MR
PROVIDER: S-EPMC4608353 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Publications
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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