Plant Pathology Department

 

Authors

Michael R. Crusoe, Michigan State University
Hussien F. Alameldin, Michigan State University
Sherine Awad, University of California, Davis
Elmar Boucher, Oregon Health and Science University
Adam Caldwell, San Jose State University
Reed Cartwright, Arizona State University
Amanda Charbonneau, Michigan State University
Bede Constantinides, University of Manchester
Greg Edvenson, Micron Technology
Scott Fay, Invitae
Jacob Fenton, Michigan State University
Thomas Fenzl, Independent Researcher
Jordan Fish, Michigan State University
Leonor Garcia-Gutierrez, University of Warwick
Phillip Garland, Eastlake Data
Jonathan Gluck, University of Maryland at College Park
Iván González, Massachusetts General Hospital
Sarah Guermond, Independent Researcher
Jiarong Guo, Michigan State University
Aditi Gupta, Michigan State University
Joshua R. Herr, Michigan State University
Adina Howe, Iowa State University
Alex Hyer, University of Utah
Andreas Härpfer, ConSol* Software GmbH
Luiz Irber, Michigan State University
Rhys Kidd, Independent Researcher
David Lin, Verdematics
Justin Lippi, Independent Researcher
Tamer Mansour, University of California, Davis & Mansoura University
Pamela McA'Nulty, Addgene
Eric McDonald, Michigan State University
Jessica Mizzi, Michigan State University
Kevin D. Murray, The Australian National University
Joshua R. Nahum, Michigan State University
Kaben Nanlohy, Independent Researcher
Alexander Johan Nederbragt, University of Oslo
Humberto Ortiz-Zuazaga, University of Puerto Rico- San Juan
Jeramia Ory, St. Louis College of Pharmacy
Jason Pell, Michigan State University
Charles Pepe-Ranney, Cornell University
Zachary N. Russ, UC Berkeley
Camille Scott, Michigan State University
Josiah Seaman, Newline Technical Innovations
Scott Sievert 38, University of Minnesota
Jared Simpson, Ontario Institute for Cancer Research & University of Toronto
Connor T. Skennerton, California Institute of Technology
James Spencer, Imperial College London
Ramakrishnan Srinivasan, Icahn School of Medicine at Mount Sinai
Daniel Standage, Indiana University & Iowa State University
James A. Stapleton, Michigan State University
Susan R. Steinman, The New York Eye and Ear Infirmary of Mount Sinai
Joe Stein, Independent Researcher
Benjamin Taylor, Michigan State University
Will Trimble, Argonne National Laboratory
Heather L. Wiencko, Trinity College Dublin, Ireland
Michael Wright, Michigan State University
Brian Wyss, Michigan State University
Qingpeng Zhang, Michigan State University
en zyme, Independent Researcher
C. Titus Brown, Michigan State University & University of California & Michigan State University
Erich Schwarz, Cornell University

Date of this Version

10-15-2015

Citation

2015 Crusoe MR et al.

Comments

Crusoe MR, Alameldin HF, Awad S et al. The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] F1000Research 2015, 4:900 (doi: 10.12688/f1000research.6924.1)

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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