The khmer software package: enabling efficient nucleotide sequence analysis

doi:10.12688/f1000research.6924.1

. 2015 Sep 25:4:900.

doi: 10.12688/f1000research.6924.1. eCollection 2015.

The khmer software package: enabling efficient nucleotide sequence analysis

Michael R Crusoe¹, Hussien F Alameldin², Sherine Awad³, Elmar Boucher⁴, Adam Caldwell⁵, Reed Cartwright⁶, Amanda Charbonneau⁷, Bede Constantinides⁸, Greg Edvenson⁹, Scott Fay¹⁰, Jacob Fenton¹¹, Thomas Fenzl¹², Jordan Fish¹¹, Leonor Garcia-Gutierrez¹³, Phillip Garland¹⁴, Jonathan Gluck¹⁵, Iván González¹⁶, Sarah Guermond¹⁷, Jiarong Guo¹⁸, Aditi Gupta¹, Joshua R Herr¹, Adina Howe¹⁹, Alex Hyer²⁰, Andreas Härpfer²¹, Luiz Irber¹¹, Rhys Kidd²², David Lin²³, Justin Lippi²⁴, Tamer Mansour²⁵, Pamela McA'Nulty²⁶, Eric McDonald¹¹, Jessica Mizzi²⁷, Kevin D Murray²⁸, Joshua R Nahum²⁹, Kaben Nanlohy³⁰, Alexander Johan Nederbragt³¹, Humberto Ortiz-Zuazaga³², Jeramia Ory³³, Jason Pell¹¹, Charles Pepe-Ranney³⁴, Zachary N Russ³⁵, Erich Schwarz³⁶, Camille Scott¹¹, Josiah Seaman³⁷, Scott Sievert³⁸, Jared Simpson³⁹, Connor T Skennerton⁴⁰, James Spencer⁴¹, Ramakrishnan Srinivasan⁴², Daniel Standage⁴³, James A Stapleton⁴⁴, Susan R Steinman⁴⁵, Joe Stein⁴⁶, Benjamin Taylor¹¹, Will Trimble⁴⁷, Heather L Wiencko⁴⁸, Michael Wright¹¹, Brian Wyss¹¹, Qingpeng Zhang¹¹, En Zyme⁴⁹, C Titus Brown⁵⁰

Affiliations

¹ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
² Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
³ Population Health and Reproduction, University of California, Davis, Davis, CA, USA.
⁴ Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
⁵ Biology Department, San Jose State University, San Jose, CA, USA.
⁶ School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
⁷ Genetics, Michigan State University, East Lansing, MI, USA.
⁸ Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
⁹ Micron Technology, Seattle, WA, USA.
¹⁰ Invitae, San Francisco, CA, USA.
¹¹ Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
¹² Independent Researcher, Munich, Germany.
¹³ Mathematics Institute, University of Warwick, Warwick, UK.
¹⁴ Eastlake Data, Seattle, WA, USA.
¹⁵ Graduate Program, University of Maryland, College Park, MD, USA.
¹⁶ Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.
¹⁷ Independent Researcher, Seattle, WA, USA.
¹⁸ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
¹⁹ Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.
²⁰ Department of Biology, University of Utah, Salt Lake City, UT, USA.
²¹ ConSol Software GmbH, Munchen, Germany.
²² Independent Researcher, Sydney, Australia.
²³ Verdematics, Fremont, CA, USA.
²⁴ Independent Researcher, San Francisco, CA, USA.
²⁵ Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Clinical Pathology, Mansoura University, Mansoura, Egypt.
²⁶ Addgene, Cambridge, MA, USA.
²⁷ Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
²⁸ ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.
²⁹ BEACON Center, Michigan State University, East Lansing, MI, USA.
³⁰ Independent Researcher, New Orleans, LA, USA.
³¹ Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.
³² Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.
³³ Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.
³⁴ Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.
³⁵ Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
³⁶ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
³⁷ Data Visualization, Newline Technical Innovations, Windsor, CO, USA.
³⁸ Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.
³⁹ Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.
⁴⁰ Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
⁴¹ Dept of Physics and Dept of Materials, Imperial College London, London, UK.
⁴² Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁴³ Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.
⁴⁴ Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA.
⁴⁵ The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.
⁴⁶ Independent Researcher, Providence, RI, USA.
⁴⁷ Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.
⁴⁸ Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.
⁴⁹ Independent Researcher, Boston, MA, USA.
⁵⁰ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA ; Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.

PMID: 26535114
PMCID: PMC4608353
DOI: 10.12688/f1000research.6924.1

The khmer software package: enabling efficient nucleotide sequence analysis

Michael R Crusoe et al. F1000Res. 2015.

. 2015 Sep 25:4:900.

doi: 10.12688/f1000research.6924.1. eCollection 2015.

Authors

Affiliations

¹ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
² Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
³ Population Health and Reproduction, University of California, Davis, Davis, CA, USA.
⁴ Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
⁵ Biology Department, San Jose State University, San Jose, CA, USA.
⁶ School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
⁷ Genetics, Michigan State University, East Lansing, MI, USA.
⁸ Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
⁹ Micron Technology, Seattle, WA, USA.
¹⁰ Invitae, San Francisco, CA, USA.
¹¹ Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
¹² Independent Researcher, Munich, Germany.
¹³ Mathematics Institute, University of Warwick, Warwick, UK.
¹⁴ Eastlake Data, Seattle, WA, USA.
¹⁵ Graduate Program, University of Maryland, College Park, MD, USA.
¹⁶ Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.
¹⁷ Independent Researcher, Seattle, WA, USA.
¹⁸ Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
¹⁹ Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.
²⁰ Department of Biology, University of Utah, Salt Lake City, UT, USA.
²¹ ConSol Software GmbH, Munchen, Germany.
²² Independent Researcher, Sydney, Australia.
²³ Verdematics, Fremont, CA, USA.
²⁴ Independent Researcher, San Francisco, CA, USA.
²⁵ Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Clinical Pathology, Mansoura University, Mansoura, Egypt.
²⁶ Addgene, Cambridge, MA, USA.
²⁷ Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
²⁸ ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.
²⁹ BEACON Center, Michigan State University, East Lansing, MI, USA.
³⁰ Independent Researcher, New Orleans, LA, USA.
³¹ Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.
³² Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.
³³ Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.
³⁴ Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.
³⁵ Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
³⁶ Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
³⁷ Data Visualization, Newline Technical Innovations, Windsor, CO, USA.
³⁸ Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.
³⁹ Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.
⁴⁰ Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
⁴¹ Dept of Physics and Dept of Materials, Imperial College London, London, UK.
⁴² Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
⁴³ Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.
⁴⁴ Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA.
⁴⁵ The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.
⁴⁶ Independent Researcher, Providence, RI, USA.
⁴⁷ Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.
⁴⁸ Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.
⁴⁹ Independent Researcher, Boston, MA, USA.
⁵⁰ Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA ; Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.

PMID: 26535114
PMCID: PMC4608353
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/.

Keywords: bioinformatics; dna sequencing analysis; k-mer; khmer; kmer; low-memory; online; streaming.

PubMed Disclaimer

Conflict of interest statement

Competing interests: No competing interests were disclosed.

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References

1. Zhang Q, Pell J, Canino-Koning R, et al. : These are not the k-mers you are looking for: Efficient online k-mer counting using a probabilistic data structure. PLoS One. 2014;9(7):e101271. 10.1371/journal.pone.0101271 - DOI - PMC - PubMed
1. Pell J, Hintze A, Canino-Koning R, et al. : Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A. 2012;109(33):13272–7. 10.1073/pnas.1121464109 - DOI - PMC - PubMed
1. Brown CT, Howe A, Zhang Q, et al. : A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv preprint.2012. Reference Source
1. Zhang Q, Awad S, Brown CT: Crossing the streams: a framework for streaming analysis of short DNA sequencing reads. PeerJ PrePrints. 2015;3:e1100 10.7287/peerj.preprints.890v1 - DOI
1. Döring A, Weese D, Rausch T, et al. : SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics. 2008;9(1):11. 10.1186/1471-2105-9-11 - DOI - PMC - PubMed

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[1] Zhang Q, Pell J, Canino-Koning R, et al. : These are not the k-mers you are looking for: Efficient online k-mer counting using a probabilistic data structure. PLoS One. 2014;9(7):e101271. 10.1371/journal.pone.0101271 - DOI - PMC - PubMed

[2] Zhang Q, Pell J, Canino-Koning R, et al. : These are not the k-mers you are looking for: Efficient online k-mer counting using a probabilistic data structure. PLoS One. 2014;9(7):e101271. 10.1371/journal.pone.0101271 - DOI - PMC - PubMed

[3] Pell J, Hintze A, Canino-Koning R, et al. : Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A. 2012;109(33):13272–7. 10.1073/pnas.1121464109 - DOI - PMC - PubMed

[4] Pell J, Hintze A, Canino-Koning R, et al. : Scaling metagenome sequence assembly with probabilistic de Bruijn graphs. Proc Natl Acad Sci U S A. 2012;109(33):13272–7. 10.1073/pnas.1121464109 - DOI - PMC - PubMed

[5] Brown CT, Howe A, Zhang Q, et al. : A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv preprint.2012. Reference Source

[6] Brown CT, Howe A, Zhang Q, et al. : A reference-free algorithm for computational normalization of shotgun sequencing data. arXiv preprint.2012. Reference Source

[7] Zhang Q, Awad S, Brown CT: Crossing the streams: a framework for streaming analysis of short DNA sequencing reads. PeerJ PrePrints. 2015;3:e1100 10.7287/peerj.preprints.890v1 - DOI

[8] Zhang Q, Awad S, Brown CT: Crossing the streams: a framework for streaming analysis of short DNA sequencing reads. PeerJ PrePrints. 2015;3:e1100 10.7287/peerj.preprints.890v1 - DOI

[9] Döring A, Weese D, Rausch T, et al. : SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics. 2008;9(1):11. 10.1186/1471-2105-9-11 - DOI - PMC - PubMed

[10] Döring A, Weese D, Rausch T, et al. : SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics. 2008;9(1):11. 10.1186/1471-2105-9-11 - DOI - PMC - PubMed

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The khmer software package: enabling efficient nucleotide sequence analysis

Affiliations

The khmer software package: enabling efficient nucleotide sequence analysis

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