Search

Scholarly Works (1 results)

Article
Peer Reviewed

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

UC Davis Previously Published Works (2015)

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/.