The khmer software package: enabling efficient nucleotide sequence analysis

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

doi:10.12688/f1000research.6924.1

Public

The khmer software package: enabling efficient nucleotide sequence analysis

Published in F1000Research • Sep 25, 2015

Authors:

Michael R. Crusoe

Hussien F. Alameldin

Sherine Awad

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 normaliza...

Subject

De Bruijn sequence

Python (programming language)

De Bruijn graph

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