The khmer software package: enabling efficient nucleotide sequence analysis [version 1; peer review: 2 approved, 1 approved with reservations]

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; peer review: 2 approved, 1 approved with reservations]

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 normaliza...

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Veröffentlicht in:F1000 research 2015, Vol.4, p.900-900
Hauptverfasser: Crusoe, Michael R, 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, Adina, 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
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Sprache:eng
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Bioinformatics
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Zusammenfassung: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/.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.6924.1