F1000Research (Sep 2015)
The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]
- 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
Affiliations
- Michael R. Crusoe
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Hussien F. Alameldin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Sherine Awad
- Population Health and Reproduction, University of California, Davis, Davis, CA, USA
- Elmar Boucher
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
- Adam Caldwell
- Biology Department, San Jose State University, San Jose, CA, USA
- Reed Cartwright
- School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Amanda Charbonneau
- Genetics, Michigan State University, East Lansing, MI, USA
- Bede Constantinides
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK
- Greg Edvenson
- Micron Technology, Seattle, WA, USA
- Scott Fay
- Invitae, San Francisco, CA, USA
- Jacob Fenton
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Thomas Fenzl
- Independent Researcher, Munich, Germany
- Jordan Fish
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Leonor Garcia-Gutierrez
- Mathematics Institute, University of Warwick, Warwick, UK
- Phillip Garland
- Eastlake Data, Seattle, WA, USA
- Jonathan Gluck
- Graduate Program, University of Maryland, College Park, MD, USA
- Iván González
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Sarah Guermond
- Independent Researcher, Seattle, WA, USA
- Jiarong Guo
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA
- Aditi Gupta
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Joshua R. Herr
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
- Alex Hyer
- Department of Biology, University of Utah, Salt Lake City, UT, USA
- Andreas Härpfer
- ConSol* Software GmbH, Munchen, Germany
- Luiz Irber
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Rhys Kidd
- Independent Researcher, Sydney, Australia
- David Lin
- Verdematics, Fremont, CA, USA
- Justin Lippi
- Independent Researcher, San Francisco, CA, USA
- Tamer Mansour
- Population Health and Reproduction, University of California, Davis, Davis, CA, USA
- Pamela McA'Nulty
- Addgene, Cambridge, MA, USA
- Eric McDonald
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Jessica Mizzi
- Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Kevin D. Murray
- ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia
- Joshua R. Nahum
- BEACON Center, Michigan State University, East Lansing, MI, USA
- Kaben Nanlohy
- Independent Researcher, New Orleans, LA, USA
- Alexander Johan Nederbragt
- Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway
- Humberto Ortiz-Zuazaga
- Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico
- Jeramia Ory
- Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA
- Jason Pell
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Charles Pepe-Ranney
- Crop and Soil Sciences, Cornell University, Ithaca, NY, USA
- Zachary N. Russ
- Department of Bioengineering, UC Berkeley, Berkeley, CA, USA
- Erich Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Camille Scott
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Josiah Seaman
- Data Visualization, Newline Technical Innovations, Windsor, CO, USA
- Scott Sievert
- Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
- Jared Simpson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- James Spencer
- Dept of Physics and Dept of Materials, Imperial College London, London, UK
- Ramakrishnan Srinivasan
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Daniel Standage
- Department of Biology, Indiana University, Bloomington, IN, USA
- James A. Stapleton
- Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA
- Susan R. Steinman
- The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA
- Joe Stein
- Independent Researcher, Providence, RI, USA
- Benjamin Taylor
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Will Trimble
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA
- Heather L. Wiencko
- Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland
- Michael Wright
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Brian Wyss
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- Qingpeng Zhang
- Computer Science and Engineering, Michigan State University, East Lansing, MI, USA
- en zyme
- Independent Researcher, Boston, MA, USA
- C. Titus Brown
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- DOI
- https://doi.org/10.12688/f1000research.6924.1
- Journal volume & issue
-
Vol. 4
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/.
Keywords
