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The khmer software package: enabling efficient nucleotide sequence analysis
- 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
- et al.
Published Web Location
http://f1000research.com/articles/4-900/v1No data is associated with this publication.
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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