The khmer software package: enabling efficient nucleotide sequence analysis.

Michael R Crusoe,Hussien F Alameldin,Sherine Awad,Elmar Boucher, Adam Caldwell,Reed Cartwright,Amanda Charbonneau,Bede Constantinides,Greg Edvenson,Scott Fay, Jacob Fenton,Thomas Fenzl,Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland,Jonathan Gluck,Iván González,Sarah Guermond,Jiarong Guo,Aditi Gupta,Joshua R Herr,Adina Howe,Alex Hyer,Andreas Härpfer,Luiz Irber, Rhys Kidd,David Lin,Justin Lippi,Tamer Mansour,Pamela McA'Nulty,Eric McDonald,Jessica Mizzi,Kevin D Murray,Joshua R Nahum,Kaben Nanlohy,Alexander Johan Nederbragt,Humberto Ortiz-Zuazaga,Jeramia Ory,Jason Pell,Charles Pepe-Ranney,Zachary N Russ,Erich Schwarz,Camille Scott,Josiah Seaman,Scott Sievert,Jared Simpson,Connor T Skennerton,James Spencer,Ramakrishnan Srinivasan,Daniel Standage,James A Stapleton, Susan R Steinman,Joe Stein,Benjamin Taylor,Will Trimble,Heather L Wiencko,Michael Wright,Brian Wyss,Qingpeng Zhang,En Zyme,C Titus Brown

F1000Research（2015）

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摘要

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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