The khmer software package: enabling efficient nucleotide sequence analysis
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Published:2015-09-25
Issue:
Volume:4
Page:900
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ISSN:2046-1402
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Container-title:F1000Research
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language:en
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Short-container-title:F1000Res
Author:
Crusoe Michael R.ORCID, Alameldin Hussien F., Awad Sherine, 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 R., Howe AdinaORCID, Hyer Alex, Härpfer Andreas, Irber Luiz, Kidd Rhys, Lin David, Lippi Justin, Mansour Tamer, McA'Nulty Pamela, McDonald Eric, Mizzi Jessica, Murray Kevin D., Nahum Joshua R., Nanlohy Kaben, Nederbragt Alexander Johan, Ortiz-Zuazaga Humberto, Ory Jeramia, Pell Jason, Pepe-Ranney Charles, Russ Zachary N., Schwarz Erich, Scott Camille, Seaman Josiah, Sievert Scott, Simpson Jared, Skennerton Connor T., Spencer James, Srinivasan Ramakrishnan, Standage Daniel, Stapleton James A., Steinman Susan R., Stein Joe, Taylor Benjamin, Trimble Will, Wiencko Heather L., Wright Michael, Wyss Brian, Zhang Qingpeng, zyme en, Brown C. Titus
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/.
Publisher
F1000 Research Ltd
Subject
General Pharmacology, Toxicology and Pharmaceutics,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine
Cited by
327 articles.
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