The khmer software package: enabling efficient nucleotide sequence analysis
Identifieur interne : 000C67 ( Pmc/Curation ); précédent : 000C66; suivant : 000C68The khmer software package: enabling efficient nucleotide sequence analysis
Auteurs : Michael R. Crusoe [États-Unis] ; Hussien F. Alameldin [États-Unis] ; Sherine Awad [États-Unis] ; Elmar Boucher [États-Unis] ; Adam Caldwell [États-Unis] ; Reed Cartwright [États-Unis] ; Amanda Charbonneau [États-Unis] ; Bede Constantinides [Royaume-Uni] ; Greg Edvenson [États-Unis] ; Scott Fay [États-Unis] ; Jacob Fenton [États-Unis] ; Thomas Fenzl [Allemagne] ; Jordan Fish [États-Unis] ; Leonor Garcia-Gutierrez [Royaume-Uni] ; Phillip Garland [États-Unis] ; Jonathan Gluck [États-Unis] ; Iván González [États-Unis] ; Sarah Guermond [États-Unis] ; Jiarong Guo [États-Unis] ; Aditi Gupta [États-Unis] ; Joshua R. Herr [États-Unis] ; Adina Howe [États-Unis] ; Alex Hyer [États-Unis] ; Andreas H Rpfer [Allemagne] ; Luiz Irber [États-Unis] ; Rhys Kidd [Australie] ; David Lin [États-Unis] ; Justin Lippi [États-Unis] ; Tamer Mansour [États-Unis, Égypte] ; Pamela Mca'Nulty [États-Unis] ; Eric Mcdonald [États-Unis] ; Jessica Mizzi [États-Unis] ; Kevin D. Murray [Australie] ; Joshua R. Nahum [États-Unis] ; Kaben Nanlohy [États-Unis] ; Alexander Johan Nederbragt [Norvège] ; Humberto Ortiz-Zuazaga [Porto Rico] ; Jeramia Ory [États-Unis] ; Jason Pell [États-Unis] ; Charles Pepe-Ranney [États-Unis] ; Zachary N. Russ [États-Unis] ; Erich Schwarz [États-Unis] ; Camille Scott [États-Unis] ; Josiah Seaman [États-Unis] ; Scott Sievert [États-Unis] ; Jared Simpson [Canada] ; Connor T. Skennerton [États-Unis] ; James Spencer [Royaume-Uni] ; Ramakrishnan Srinivasan [États-Unis] ; Daniel Standage [États-Unis] ; James A. Stapleton [États-Unis] ; Susan R. Steinman [États-Unis] ; Joe Stein [États-Unis] ; Benjamin Taylor [États-Unis] ; Will Trimble [États-Unis] ; Heather L. Wiencko [Irlande (pays)] ; Michael Wright [États-Unis] ; Brian Wyss [États-Unis] ; Qingpeng Zhang [États-Unis] ; En Zyme [États-Unis] ; C. Titus Brown [États-Unis]Source :
- F1000Research [ 2046-1402 ] ; 2015.
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
Url:
DOI: 10.12688/f1000research.6924.1
PubMed: 26535114
PubMed Central: 4608353
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Russ</name><affiliation wicri:level="1"><nlm:aff id="a35">Department of Bioengineering, UC Berkeley, Berkeley, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, UC Berkeley, Berkeley, CA</wicri:regionArea></affiliation></author><author><name sortKey="Schwarz, Erich" sort="Schwarz, Erich" uniqKey="Schwarz E" first="Erich" last="Schwarz">Erich Schwarz</name><affiliation wicri:level="1"><nlm:aff id="a36">Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY</wicri:regionArea></affiliation></author><author><name sortKey="Scott, Camille" sort="Scott, Camille" uniqKey="Scott C" first="Camille" last="Scott">Camille Scott</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Seaman, Josiah" sort="Seaman, Josiah" uniqKey="Seaman J" first="Josiah" last="Seaman">Josiah Seaman</name><affiliation wicri:level="1"><nlm:aff id="a37">Data Visualization, Newline Technical Innovations, Windsor, CO, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Data Visualization, Newline Technical Innovations, Windsor, CO</wicri:regionArea></affiliation></author><author><name sortKey="Sievert, Scott" sort="Sievert, Scott" uniqKey="Sievert S" first="Scott" last="Sievert">Scott Sievert</name><affiliation wicri:level="1"><nlm:aff id="a38">Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN</wicri:regionArea></affiliation></author><author><name sortKey="Simpson, Jared" sort="Simpson, Jared" uniqKey="Simpson J" first="Jared" last="Simpson">Jared Simpson</name><affiliation wicri:level="1"><nlm:aff id="a39">Ontario Institute for Cancer Research, Toronto, ON, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, Toronto, ON</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a40">Computer Science, University of Toronto, Toronto, ON, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Computer Science, University of Toronto, Toronto, ON</wicri:regionArea></affiliation></author><author><name sortKey="Skennerton, Connor T" sort="Skennerton, Connor T" uniqKey="Skennerton C" first="Connor T." last="Skennerton">Connor T. 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Wiencko</name><affiliation wicri:level="1"><nlm:aff id="a50">Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Wright, Michael" sort="Wright, Michael" uniqKey="Wright M" first="Michael" last="Wright">Michael Wright</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Wyss, Brian" sort="Wyss, Brian" uniqKey="Wyss B" first="Brian" last="Wyss">Brian Wyss</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Qingpeng" sort="Zhang, Qingpeng" uniqKey="Zhang Q" first="Qingpeng" last="Zhang">Qingpeng Zhang</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Zyme, En" sort="Zyme, En" uniqKey="Zyme E" first="En" last="Zyme">En Zyme</name><affiliation wicri:level="1"><nlm:aff id="a51">Independent Researcher, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, Boston, MA</wicri:regionArea></affiliation></author><author><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><affiliation wicri:level="1"><nlm:aff id="a1">Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3">Population Health and Reproduction, University of California, Davis, Davis, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis, Davis, CA</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26535114</idno><idno type="pmc">4608353</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608353</idno><idno type="RBID">PMC:4608353</idno><idno type="doi">10.12688/f1000research.6924.1</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000C67</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000C67</idno><idno type="wicri:Area/Pmc/Curation">000C67</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000C67</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The khmer software package: enabling efficient nucleotide sequence analysis</title><author><name sortKey="Crusoe, Michael R" sort="Crusoe, Michael R" uniqKey="Crusoe M" first="Michael R." last="Crusoe">Michael R. Crusoe</name><affiliation wicri:level="1"><nlm:aff id="a1">Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Alameldin, Hussien F" sort="Alameldin, Hussien F" uniqKey="Alameldin H" first="Hussien F." last="Alameldin">Hussien F. Alameldin</name><affiliation wicri:level="1"><nlm:aff id="a2">Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Awad, Sherine" sort="Awad, Sherine" uniqKey="Awad S" first="Sherine" last="Awad">Sherine Awad</name><affiliation wicri:level="1"><nlm:aff id="a3">Population Health and Reproduction, University of California, Davis, Davis, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis, Davis, CA</wicri:regionArea></affiliation></author><author><name sortKey="Boucher, Elmar" sort="Boucher, Elmar" uniqKey="Boucher E" first="Elmar" last="Boucher">Elmar Boucher</name><affiliation wicri:level="1"><nlm:aff id="a4">Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR</wicri:regionArea></affiliation></author><author><name sortKey="Caldwell, Adam" sort="Caldwell, Adam" uniqKey="Caldwell A" first="Adam" last="Caldwell">Adam Caldwell</name><affiliation wicri:level="1"><nlm:aff id="a5">Biology Department, San Jose State University, San Jose, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biology Department, San Jose State University, San Jose, CA</wicri:regionArea></affiliation></author><author><name sortKey="Cartwright, Reed" sort="Cartwright, Reed" uniqKey="Cartwright R" first="Reed" last="Cartwright">Reed Cartwright</name><affiliation wicri:level="1"><nlm:aff id="a6">School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ</wicri:regionArea></affiliation></author><author><name sortKey="Charbonneau, Amanda" sort="Charbonneau, Amanda" uniqKey="Charbonneau A" first="Amanda" last="Charbonneau">Amanda Charbonneau</name><affiliation wicri:level="1"><nlm:aff id="a7">Genetics, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genetics, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Constantinides, Bede" sort="Constantinides, Bede" uniqKey="Constantinides B" first="Bede" last="Constantinides">Bede Constantinides</name><affiliation wicri:level="1"><nlm:aff id="a8">Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester</wicri:regionArea></affiliation></author><author><name sortKey="Edvenson, Greg" sort="Edvenson, Greg" uniqKey="Edvenson G" first="Greg" last="Edvenson">Greg Edvenson</name><affiliation wicri:level="1"><nlm:aff id="a9">Micron Technology, Seattle, WA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Micron Technology, Seattle, WA</wicri:regionArea></affiliation></author><author><name sortKey="Fay, Scott" sort="Fay, Scott" uniqKey="Fay S" first="Scott" last="Fay">Scott Fay</name><affiliation wicri:level="1"><nlm:aff id="a10">Invitae, San Francisco, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Invitae, San Francisco, CA</wicri:regionArea></affiliation></author><author><name sortKey="Fenton, Jacob" sort="Fenton, Jacob" uniqKey="Fenton J" first="Jacob" last="Fenton">Jacob Fenton</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Fenzl, Thomas" sort="Fenzl, Thomas" uniqKey="Fenzl T" first="Thomas" last="Fenzl">Thomas Fenzl</name><affiliation wicri:level="1"><nlm:aff id="a12">Independent Researcher, Munich, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Independent Researcher, Munich</wicri:regionArea></affiliation></author><author><name sortKey="Fish, Jordan" sort="Fish, Jordan" uniqKey="Fish J" first="Jordan" last="Fish">Jordan Fish</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Garcia Gutierrez, Leonor" sort="Garcia Gutierrez, Leonor" uniqKey="Garcia Gutierrez L" first="Leonor" last="Garcia-Gutierrez">Leonor Garcia-Gutierrez</name><affiliation wicri:level="1"><nlm:aff id="a13">Mathematics Institute, University of Warwick, Warwick, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Mathematics Institute, University of Warwick, Warwick</wicri:regionArea></affiliation></author><author><name sortKey="Garland, Phillip" sort="Garland, Phillip" uniqKey="Garland P" first="Phillip" last="Garland">Phillip Garland</name><affiliation wicri:level="1"><nlm:aff id="a14">Eastlake Data, Seattle, WA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Eastlake Data, Seattle, WA</wicri:regionArea></affiliation></author><author><name sortKey="Gluck, Jonathan" sort="Gluck, Jonathan" uniqKey="Gluck J" first="Jonathan" last="Gluck">Jonathan Gluck</name><affiliation wicri:level="1"><nlm:aff id="a15">Graduate Program, University of Maryland, College Park, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Graduate Program, University of Maryland, College Park, MD</wicri:regionArea></affiliation></author><author><name sortKey="Gonzalez, Ivan" sort="Gonzalez, Ivan" uniqKey="Gonzalez I" first="Iván" last="González">Iván González</name><affiliation wicri:level="1"><nlm:aff id="a16">Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA</wicri:regionArea></affiliation></author><author><name sortKey="Guermond, Sarah" sort="Guermond, Sarah" uniqKey="Guermond S" first="Sarah" last="Guermond">Sarah Guermond</name><affiliation wicri:level="1"><nlm:aff id="a17">Independent Researcher, Seattle, WA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, Seattle, WA</wicri:regionArea></affiliation></author><author><name sortKey="Guo, Jiarong" sort="Guo, Jiarong" uniqKey="Guo J" first="Jiarong" last="Guo">Jiarong Guo</name><affiliation wicri:level="1"><nlm:aff id="a18">Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Microbial Ecology, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Gupta, Aditi" sort="Gupta, Aditi" uniqKey="Gupta A" first="Aditi" last="Gupta">Aditi Gupta</name><affiliation wicri:level="1"><nlm:aff id="a1">Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Herr, Joshua R" sort="Herr, Joshua R" uniqKey="Herr J" first="Joshua R." last="Herr">Joshua R. 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City, UT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of Utah, Salt Lake City, UT</wicri:regionArea></affiliation></author><author><name sortKey="H Rpfer, Andreas" sort="H Rpfer, Andreas" uniqKey="H Rpfer A" first="Andreas" last="H Rpfer">Andreas H Rpfer</name><affiliation wicri:level="1"><nlm:aff id="a21">ConSol* Software GmbH, Munchen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>ConSol* Software GmbH, Munchen</wicri:regionArea></affiliation></author><author><name sortKey="Irber, Luiz" sort="Irber, Luiz" uniqKey="Irber L" first="Luiz" last="Irber">Luiz Irber</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Kidd, Rhys" sort="Kidd, Rhys" uniqKey="Kidd R" first="Rhys" last="Kidd">Rhys Kidd</name><affiliation wicri:level="1"><nlm:aff id="a22">Independent Researcher, Sydney, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Independent Researcher, Sydney</wicri:regionArea></affiliation></author><author><name sortKey="Lin, David" sort="Lin, David" uniqKey="Lin D" first="David" last="Lin">David Lin</name><affiliation wicri:level="1"><nlm:aff id="a23">Verdematics, Fremont, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Verdematics, Fremont, CA</wicri:regionArea></affiliation></author><author><name sortKey="Lippi, Justin" sort="Lippi, Justin" uniqKey="Lippi J" first="Justin" last="Lippi">Justin Lippi</name><affiliation wicri:level="1"><nlm:aff id="a24">Independent Researcher, San Francisco, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, San Francisco, CA</wicri:regionArea></affiliation></author><author><name sortKey="Mansour, Tamer" sort="Mansour, Tamer" uniqKey="Mansour T" first="Tamer" last="Mansour">Tamer Mansour</name><affiliation wicri:level="1"><nlm:aff id="a3">Population Health and Reproduction, University of California, Davis, Davis, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis, Davis, CA</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a25">Clinical Pathology, Mansoura University, Mansoura, Egypt</nlm:aff><country xml:lang="fr">Égypte</country><wicri:regionArea>Clinical Pathology, Mansoura University, Mansoura</wicri:regionArea></affiliation></author><author><name sortKey="Mca Nulty, Pamela" sort="Mca Nulty, Pamela" uniqKey="Mca Nulty P" first="Pamela" last="Mca'Nulty">Pamela Mca'Nulty</name><affiliation wicri:level="1"><nlm:aff id="a26">Addgene, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Addgene, Cambridge, MA</wicri:regionArea></affiliation></author><author><name sortKey="Mcdonald, Eric" sort="Mcdonald, Eric" uniqKey="Mcdonald E" first="Eric" last="Mcdonald">Eric Mcdonald</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Mizzi, Jessica" sort="Mizzi, Jessica" uniqKey="Mizzi J" first="Jessica" last="Mizzi">Jessica Mizzi</name><affiliation wicri:level="1"><nlm:aff id="a27">Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Murray, Kevin D" sort="Murray, Kevin D" uniqKey="Murray K" first="Kevin D." last="Murray">Kevin D. Murray</name><affiliation wicri:level="1"><nlm:aff id="a28">ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT</wicri:regionArea></affiliation></author><author><name sortKey="Nahum, Joshua R" sort="Nahum, Joshua R" uniqKey="Nahum J" first="Joshua R." last="Nahum">Joshua R. Nahum</name><affiliation wicri:level="1"><nlm:aff id="a29">BEACON Center, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>BEACON Center, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Nanlohy, Kaben" sort="Nanlohy, Kaben" uniqKey="Nanlohy K" first="Kaben" last="Nanlohy">Kaben Nanlohy</name><affiliation wicri:level="1"><nlm:aff id="a30">Independent Researcher, New Orleans, LA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, New Orleans, LA</wicri:regionArea></affiliation></author><author><name sortKey="Nederbragt, Alexander Johan" sort="Nederbragt, Alexander Johan" uniqKey="Nederbragt A" first="Alexander Johan" last="Nederbragt">Alexander Johan Nederbragt</name><affiliation wicri:level="1"><nlm:aff id="a31">Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway</nlm:aff><country xml:lang="fr">Norvège</country><wicri:regionArea>Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo</wicri:regionArea></affiliation></author><author><name sortKey="Ortiz Zuazaga, Humberto" sort="Ortiz Zuazaga, Humberto" uniqKey="Ortiz Zuazaga H" first="Humberto" last="Ortiz-Zuazaga">Humberto Ortiz-Zuazaga</name><affiliation wicri:level="1"><nlm:aff id="a32">Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico</nlm:aff><country xml:lang="fr">Porto Rico</country><wicri:regionArea>Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan</wicri:regionArea></affiliation></author><author><name sortKey="Ory, Jeramia" sort="Ory, Jeramia" uniqKey="Ory J" first="Jeramia" last="Ory">Jeramia Ory</name><affiliation wicri:level="1"><nlm:aff id="a33">Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biochemistry, St. Louis College of Pharmacy, St. Louis, MO</wicri:regionArea></affiliation></author><author><name sortKey="Pell, Jason" sort="Pell, Jason" uniqKey="Pell J" first="Jason" last="Pell">Jason Pell</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Pepe Ranney, Charles" sort="Pepe Ranney, Charles" uniqKey="Pepe Ranney C" first="Charles" last="Pepe-Ranney">Charles Pepe-Ranney</name><affiliation wicri:level="1"><nlm:aff id="a34">Crop and Soil Sciences, Cornell University, Ithaca, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Crop and Soil Sciences, Cornell University, Ithaca, NY</wicri:regionArea></affiliation></author><author><name sortKey="Russ, Zachary N" sort="Russ, Zachary N" uniqKey="Russ Z" first="Zachary N." last="Russ">Zachary N. Russ</name><affiliation wicri:level="1"><nlm:aff id="a35">Department of Bioengineering, UC Berkeley, Berkeley, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioengineering, UC Berkeley, Berkeley, CA</wicri:regionArea></affiliation></author><author><name sortKey="Schwarz, Erich" sort="Schwarz, Erich" uniqKey="Schwarz E" first="Erich" last="Schwarz">Erich Schwarz</name><affiliation wicri:level="1"><nlm:aff id="a36">Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY</wicri:regionArea></affiliation></author><author><name sortKey="Scott, Camille" sort="Scott, Camille" uniqKey="Scott C" first="Camille" last="Scott">Camille Scott</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Seaman, Josiah" sort="Seaman, Josiah" uniqKey="Seaman J" first="Josiah" last="Seaman">Josiah Seaman</name><affiliation wicri:level="1"><nlm:aff id="a37">Data Visualization, Newline Technical Innovations, Windsor, CO, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Data Visualization, Newline Technical Innovations, Windsor, CO</wicri:regionArea></affiliation></author><author><name sortKey="Sievert, Scott" sort="Sievert, Scott" uniqKey="Sievert S" first="Scott" last="Sievert">Scott Sievert</name><affiliation wicri:level="1"><nlm:aff id="a38">Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN</wicri:regionArea></affiliation></author><author><name sortKey="Simpson, Jared" sort="Simpson, Jared" uniqKey="Simpson J" first="Jared" last="Simpson">Jared Simpson</name><affiliation wicri:level="1"><nlm:aff id="a39">Ontario Institute for Cancer Research, Toronto, ON, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, Toronto, ON</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a40">Computer Science, University of Toronto, Toronto, ON, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Computer Science, University of Toronto, Toronto, ON</wicri:regionArea></affiliation></author><author><name sortKey="Skennerton, Connor T" sort="Skennerton, Connor T" uniqKey="Skennerton C" first="Connor T." last="Skennerton">Connor T. Skennerton</name><affiliation wicri:level="1"><nlm:aff id="a41">Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA</wicri:regionArea></affiliation></author><author><name sortKey="Spencer, James" sort="Spencer, James" uniqKey="Spencer J" first="James" last="Spencer">James Spencer</name><affiliation wicri:level="1"><nlm:aff id="a42">Dept of Physics and Dept of Materials, Imperial College London, London, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Dept of Physics and Dept of Materials, Imperial College London, London</wicri:regionArea></affiliation></author><author><name sortKey="Srinivasan, Ramakrishnan" sort="Srinivasan, Ramakrishnan" uniqKey="Srinivasan R" first="Ramakrishnan" last="Srinivasan">Ramakrishnan Srinivasan</name><affiliation wicri:level="1"><nlm:aff id="a43">Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY</wicri:regionArea></affiliation></author><author><name sortKey="Standage, Daniel" sort="Standage, Daniel" uniqKey="Standage D" first="Daniel" last="Standage">Daniel Standage</name><affiliation wicri:level="1"><nlm:aff id="a44">Department of Biology, Indiana University, Bloomington, IN, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Indiana University, Bloomington, IN</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a45">Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA</wicri:regionArea></affiliation></author><author><name sortKey="Stapleton, James A" sort="Stapleton, James A" uniqKey="Stapleton J" first="James A." last="Stapleton">James A. Stapleton</name><affiliation wicri:level="1"><nlm:aff id="a46">Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS</wicri:regionArea></affiliation></author><author><name sortKey="Steinman, Susan R" sort="Steinman, Susan R" uniqKey="Steinman S" first="Susan R." last="Steinman">Susan R. Steinman</name><affiliation wicri:level="1"><nlm:aff id="a47">The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The New York Eye and Ear Infirmary of Mount Sinai, New York, NY</wicri:regionArea></affiliation></author><author><name sortKey="Stein, Joe" sort="Stein, Joe" uniqKey="Stein J" first="Joe" last="Stein">Joe Stein</name><affiliation wicri:level="1"><nlm:aff id="a48">Independent Researcher, Providence, RI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, Providence, RI</wicri:regionArea></affiliation></author><author><name sortKey="Taylor, Benjamin" sort="Taylor, Benjamin" uniqKey="Taylor B" first="Benjamin" last="Taylor">Benjamin Taylor</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Trimble, Will" sort="Trimble, Will" uniqKey="Trimble W" first="Will" last="Trimble">Will Trimble</name><affiliation wicri:level="1"><nlm:aff id="a49">Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL</wicri:regionArea></affiliation></author><author><name sortKey="Wiencko, Heather L" sort="Wiencko, Heather L" uniqKey="Wiencko H" first="Heather L." last="Wiencko">Heather L. Wiencko</name><affiliation wicri:level="1"><nlm:aff id="a50">Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin</wicri:regionArea></affiliation></author><author><name sortKey="Wright, Michael" sort="Wright, Michael" uniqKey="Wright M" first="Michael" last="Wright">Michael Wright</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Wyss, Brian" sort="Wyss, Brian" uniqKey="Wyss B" first="Brian" last="Wyss">Brian Wyss</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Zhang, Qingpeng" sort="Zhang, Qingpeng" uniqKey="Zhang Q" first="Qingpeng" last="Zhang">Qingpeng Zhang</name><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author><author><name sortKey="Zyme, En" sort="Zyme, En" uniqKey="Zyme E" first="En" last="Zyme">En Zyme</name><affiliation wicri:level="1"><nlm:aff id="a51">Independent Researcher, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Independent Researcher, Boston, MA</wicri:regionArea></affiliation></author><author><name sortKey="Brown, C Titus" sort="Brown, C Titus" uniqKey="Brown C" first="C. Titus" last="Brown">C. Titus Brown</name><affiliation wicri:level="1"><nlm:aff id="a1">Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a3">Population Health and Reproduction, University of California, Davis, Davis, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis, Davis, CA</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a11">Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science and Engineering, Michigan State University, East Lansing, MI</wicri:regionArea></affiliation></author></analytic><series><title level="j">F1000Research</title><idno type="eISSN">2046-1402</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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
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<front><journal-meta><journal-id journal-id-type="nlm-ta">F1000Res</journal-id><journal-id journal-id-type="iso-abbrev">F1000Res</journal-id><journal-id journal-id-type="pmc">F1000Research</journal-id><journal-title-group><journal-title>F1000Research</journal-title></journal-title-group><issn pub-type="epub">2046-1402</issn><publisher><publisher-name>F1000Research</publisher-name><publisher-loc>London, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26535114</article-id><article-id pub-id-type="pmc">4608353</article-id><article-id pub-id-type="doi">10.12688/f1000research.6924.1</article-id><article-categories><subj-group subj-group-type="heading"><subject>Software Tool Article</subject></subj-group><subj-group><subject>Articles</subject><subj-group><subject>Bioinformatics</subject></subj-group></subj-group></article-categories><title-group><article-title>The khmer software package: enabling efficient nucleotide sequence analysis</article-title><fn-group content-type="pub-status"><fn><p>[version 1; referees: 2 approved</p></fn></fn-group></title-group><contrib-group><contrib contrib-type="author"><name><surname>Crusoe</surname><given-names>Michael R.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Alameldin</surname><given-names>Hussien F.</given-names></name><xref ref-type="aff" rid="a2">2</xref></contrib><contrib contrib-type="author"><name><surname>Awad</surname><given-names>Sherine</given-names></name><xref ref-type="aff" rid="a3">3</xref></contrib><contrib contrib-type="author"><name><surname>Boucher</surname><given-names>Elmar</given-names></name><xref ref-type="aff" rid="a4">4</xref></contrib><contrib contrib-type="author"><name><surname>Caldwell</surname><given-names>Adam</given-names></name><xref ref-type="aff" rid="a5">5</xref></contrib><contrib contrib-type="author"><name><surname>Cartwright</surname><given-names>Reed</given-names></name><xref ref-type="aff" rid="a6">6</xref></contrib><contrib contrib-type="author"><name><surname>Charbonneau</surname><given-names>Amanda</given-names></name><xref ref-type="aff" rid="a7">7</xref></contrib><contrib contrib-type="author"><name><surname>Constantinides</surname><given-names>Bede</given-names></name><xref ref-type="aff" rid="a8">8</xref></contrib><contrib contrib-type="author"><name><surname>Edvenson</surname><given-names>Greg</given-names></name><xref ref-type="aff" rid="a9">9</xref></contrib><contrib contrib-type="author"><name><surname>Fay</surname><given-names>Scott</given-names></name><xref ref-type="aff" rid="a10">10</xref></contrib><contrib contrib-type="author"><name><surname>Fenton</surname><given-names>Jacob</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Fenzl</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="a12">12</xref></contrib><contrib contrib-type="author"><name><surname>Fish</surname><given-names>Jordan</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Garcia-Gutierrez</surname><given-names>Leonor</given-names></name><xref ref-type="aff" rid="a13">13</xref></contrib><contrib contrib-type="author"><name><surname>Garland</surname><given-names>Phillip</given-names></name><xref ref-type="aff" rid="a14">14</xref></contrib><contrib contrib-type="author"><name><surname>Gluck</surname><given-names>Jonathan</given-names></name><xref ref-type="aff" rid="a15">15</xref></contrib><contrib contrib-type="author"><name><surname>González</surname><given-names>Iván</given-names></name><xref ref-type="aff" rid="a16">16</xref></contrib><contrib contrib-type="author"><name><surname>Guermond</surname><given-names>Sarah</given-names></name><xref ref-type="aff" rid="a17">17</xref></contrib><contrib contrib-type="author"><name><surname>Guo</surname><given-names>Jiarong</given-names></name><xref ref-type="aff" rid="a18">18</xref></contrib><contrib contrib-type="author"><name><surname>Gupta</surname><given-names>Aditi</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Herr</surname><given-names>Joshua R.</given-names></name><xref ref-type="aff" rid="a1">1</xref></contrib><contrib contrib-type="author"><name><surname>Howe</surname><given-names>Adina</given-names></name><xref ref-type="aff" rid="a19">19</xref></contrib><contrib contrib-type="author"><name><surname>Hyer</surname><given-names>Alex</given-names></name><xref ref-type="aff" rid="a20">20</xref></contrib><contrib contrib-type="author"><name><surname>Härpfer</surname><given-names>Andreas</given-names></name><xref ref-type="aff" rid="a21">21</xref></contrib><contrib contrib-type="author"><name><surname>Irber</surname><given-names>Luiz</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Kidd</surname><given-names>Rhys</given-names></name><xref ref-type="aff" rid="a22">22</xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>David</given-names></name><xref ref-type="aff" rid="a23">23</xref></contrib><contrib contrib-type="author"><name><surname>Lippi</surname><given-names>Justin</given-names></name><xref ref-type="aff" rid="a24">24</xref></contrib><contrib contrib-type="author"><name><surname>Mansour</surname><given-names>Tamer</given-names></name><xref ref-type="aff" rid="a3">3</xref><xref ref-type="aff" rid="a25">25</xref></contrib><contrib contrib-type="author"><name><surname>McA'Nulty</surname><given-names>Pamela</given-names></name><xref ref-type="aff" rid="a26">26</xref></contrib><contrib contrib-type="author"><name><surname>McDonald</surname><given-names>Eric</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Mizzi</surname><given-names>Jessica</given-names></name><xref ref-type="aff" rid="a27">27</xref></contrib><contrib contrib-type="author"><name><surname>Murray</surname><given-names>Kevin D.</given-names></name><xref ref-type="aff" rid="a28">28</xref></contrib><contrib contrib-type="author"><name><surname>Nahum</surname><given-names>Joshua R.</given-names></name><xref ref-type="aff" rid="a29">29</xref></contrib><contrib contrib-type="author"><name><surname>Nanlohy</surname><given-names>Kaben</given-names></name><xref ref-type="aff" rid="a30">30</xref></contrib><contrib contrib-type="author"><name><surname>Nederbragt</surname><given-names>Alexander Johan</given-names></name><xref ref-type="aff" rid="a31">31</xref></contrib><contrib contrib-type="author"><name><surname>Ortiz-Zuazaga</surname><given-names>Humberto</given-names></name><xref ref-type="aff" rid="a32">32</xref></contrib><contrib contrib-type="author"><name><surname>Ory</surname><given-names>Jeramia</given-names></name><xref ref-type="aff" rid="a33">33</xref></contrib><contrib contrib-type="author"><name><surname>Pell</surname><given-names>Jason</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Pepe-Ranney</surname><given-names>Charles</given-names></name><xref ref-type="aff" rid="a34">34</xref></contrib><contrib contrib-type="author"><name><surname>Russ</surname><given-names>Zachary N.</given-names></name><xref ref-type="aff" rid="a35">35</xref></contrib><contrib contrib-type="author"><name><surname>Schwarz</surname><given-names>Erich</given-names></name><xref ref-type="aff" rid="a36">36</xref></contrib><contrib contrib-type="author"><name><surname>Scott</surname><given-names>Camille</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Seaman</surname><given-names>Josiah</given-names></name><xref ref-type="aff" rid="a37">37</xref></contrib><contrib contrib-type="author"><name><surname>Sievert</surname><given-names>Scott</given-names></name><xref ref-type="aff" rid="a38">38</xref></contrib><contrib contrib-type="author"><name><surname>Simpson</surname><given-names>Jared</given-names></name><xref ref-type="aff" rid="a39">39</xref><xref ref-type="aff" rid="a40">40</xref></contrib><contrib contrib-type="author"><name><surname>Skennerton</surname><given-names>Connor T.</given-names></name><xref ref-type="aff" rid="a41">41</xref></contrib><contrib contrib-type="author"><name><surname>Spencer</surname><given-names>James</given-names></name><xref ref-type="aff" rid="a42">42</xref></contrib><contrib contrib-type="author"><name><surname>Srinivasan</surname><given-names>Ramakrishnan</given-names></name><xref ref-type="aff" rid="a43">43</xref></contrib><contrib contrib-type="author"><name><surname>Standage</surname><given-names>Daniel</given-names></name><xref ref-type="aff" rid="a44">44</xref><xref ref-type="aff" rid="a45">45</xref></contrib><contrib contrib-type="author"><name><surname>Stapleton</surname><given-names>James A.</given-names></name><xref ref-type="aff" rid="a46">46</xref></contrib><contrib contrib-type="author"><name><surname>Steinman</surname><given-names>Susan R.</given-names></name><xref ref-type="aff" rid="a47">47</xref></contrib><contrib contrib-type="author"><name><surname>Stein</surname><given-names>Joe</given-names></name><xref ref-type="aff" rid="a48">48</xref></contrib><contrib contrib-type="author"><name><surname>Taylor</surname><given-names>Benjamin</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Trimble</surname><given-names>Will</given-names></name><xref ref-type="aff" rid="a49">49</xref></contrib><contrib contrib-type="author"><name><surname>Wiencko</surname><given-names>Heather L.</given-names></name><xref ref-type="aff" rid="a50">50</xref></contrib><contrib contrib-type="author"><name><surname>Wright</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Wyss</surname><given-names>Brian</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Qingpeng</given-names></name><xref ref-type="aff" rid="a11">11</xref></contrib><contrib contrib-type="author"><name><surname>zyme</surname><given-names>en</given-names></name><xref ref-type="aff" rid="a51">51</xref></contrib><contrib contrib-type="author"><name><surname>Brown</surname><given-names>C. Titus</given-names></name><xref ref-type="corresp" rid="c1">a</xref><xref ref-type="aff" rid="a1">1</xref><xref ref-type="aff" rid="a3">3</xref><xref ref-type="aff" rid="a11">11</xref></contrib><aff id="a1"><label>1</label>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA</aff><aff id="a2"><label>2</label>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA</aff><aff id="a3"><label>3</label>Population Health and Reproduction, University of California, Davis, Davis, CA, USA</aff><aff id="a4"><label>4</label>Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA</aff><aff id="a5"><label>5</label>Biology Department, San Jose State University, San Jose, CA, USA</aff><aff id="a6"><label>6</label>School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA</aff><aff id="a7"><label>7</label>Genetics, Michigan State University, East Lansing, MI, USA</aff><aff id="a8"><label>8</label>Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK</aff><aff id="a9"><label>9</label>Micron Technology, Seattle, WA, USA</aff><aff id="a10"><label>10</label>Invitae, San Francisco, CA, USA</aff><aff id="a11"><label>11</label>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA</aff><aff id="a12"><label>12</label>Independent Researcher, Munich, Germany</aff><aff id="a13"><label>13</label>Mathematics Institute, University of Warwick, Warwick, UK</aff><aff id="a14"><label>14</label>Eastlake Data, Seattle, WA, USA</aff><aff id="a15"><label>15</label>Graduate Program, University of Maryland, College Park, MD, USA</aff><aff id="a16"><label>16</label>Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA</aff><aff id="a17"><label>17</label>Independent Researcher, Seattle, WA, USA</aff><aff id="a18"><label>18</label>Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA</aff><aff id="a19"><label>19</label>Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA</aff><aff id="a20"><label>20</label>Department of Biology, University of Utah, Salt Lake City, UT, USA</aff><aff id="a21"><label>21</label>ConSol* Software GmbH, Munchen, Germany</aff><aff id="a22"><label>22</label>Independent Researcher, Sydney, Australia</aff><aff id="a23"><label>23</label>Verdematics, Fremont, CA, USA</aff><aff id="a24"><label>24</label>Independent Researcher, San Francisco, CA, USA</aff><aff id="a25"><label>25</label>Clinical Pathology, Mansoura University, Mansoura, Egypt</aff><aff id="a26"><label>26</label>Addgene, Cambridge, MA, USA</aff><aff id="a27"><label>27</label>Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA</aff><aff id="a28"><label>28</label>ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia</aff><aff id="a29"><label>29</label>BEACON Center, Michigan State University, East Lansing, MI, USA</aff><aff id="a30"><label>30</label>Independent Researcher, New Orleans, LA, USA</aff><aff id="a31"><label>31</label>Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway</aff><aff id="a32"><label>32</label>Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico</aff><aff id="a33"><label>33</label>Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA</aff><aff id="a34"><label>34</label>Crop and Soil Sciences, Cornell University, Ithaca, NY, USA</aff><aff id="a35"><label>35</label>Department of Bioengineering, UC Berkeley, Berkeley, CA, USA</aff><aff id="a36"><label>36</label>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA</aff><aff id="a37"><label>37</label>Data Visualization, Newline Technical Innovations, Windsor, CO, USA</aff><aff id="a38"><label>38</label>Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA</aff><aff id="a39"><label>39</label>Ontario Institute for Cancer Research, Toronto, ON, Canada</aff><aff id="a40"><label>40</label>Computer Science, University of Toronto, Toronto, ON, Canada</aff><aff id="a41"><label>41</label>Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA</aff><aff id="a42"><label>42</label>Dept of Physics and Dept of Materials, Imperial College London, London, UK</aff><aff id="a43"><label>43</label>Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA</aff><aff id="a44"><label>44</label>Department of Biology, Indiana University, Bloomington, IN, USA</aff><aff id="a45"><label>45</label>Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA</aff><aff id="a46"><label>46</label>Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA</aff><aff id="a47"><label>47</label>The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA</aff><aff id="a48"><label>48</label>Independent Researcher, Providence, RI, USA</aff><aff id="a49"><label>49</label>Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA</aff><aff id="a50"><label>50</label>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland</aff><aff id="a51"><label>51</label>Independent Researcher, Boston, MA, USA</aff></contrib-group><author-notes><corresp id="c1"><label>a</label><email xlink:href="mailto:titus@idyll.org">titus@idyll.org</email></corresp><fn fn-type="con"><p>CTB is the primary investigator for the khmer software package. MRC is the lead software developer from July 2013 onwards. Many significant components of khmer have their own paper describing them (see “Use Cases”, above). The remaining authors each have one or more Git commits in their name.</p></fn><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>25</day><month>9</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>4</volume><elocation-id>900</elocation-id><history><date date-type="accepted"><day>25</day><month>9</month><year>2015</year></date></history><permissions><copyright-statement>Copyright: © 2015 Crusoe MR et al.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="f1000research-4-7456.pdf"></self-uri><abstract><p>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
<ext-link ext-link-type="uri" xlink:href="https://github.com/dib-lab/khmer/">https://github.com/dib-lab/khmer/</ext-link>.</p></abstract><kwd-group kwd-group-type="author"><kwd>bioinformatics</kwd><kwd>dna sequencing analysis</kwd><kwd>k-mer</kwd><kwd>kmer</kwd><kwd>khmer</kwd><kwd>online</kwd><kwd>low-memory</kwd><kwd>streaming</kwd></kwd-group><funding-group><award-group id="fund-1"><funding-source>USDA NIFA</funding-source><award-id>2010-65205-20361</award-id></award-group><award-group id="fund-2"><funding-source>National Institutes of Health</funding-source><award-id>R01HG007513</award-id></award-group><award-group id="fund-3"><funding-source>Gordon and Betty Moore Foundation</funding-source><award-id>GBMF4551</award-id></award-group><funding-statement>khmer development has largely been supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is now funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513, as well as by the the Gordon and Betty Moore Foundation under Award number GBMF4551, all to CTB.</funding-statement><funding-statement><italic>I confirm that the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</italic></funding-statement></funding-group></article-meta></front><sub-article id="report10508" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.7456.r10508</article-id><title-group><article-title>Referee response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Patro</surname><given-names>Rob</given-names></name><xref ref-type="aff" rid="r10508a1">1</xref><role>Referee</role></contrib><aff id="r10508a1"><label>1</label>Computer Science Department, Stony Brook University, Stony Brook, NY, USA</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>8</day><month>10</month><year>2015</year></pub-date><related-article id="d35e1925" related-article-type="peer-reviewed-article" ext-link-type="doi" xlink:href="10.12688/f1000research.6924.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>This paper describes version 2 of the khmer software suite. The software is developed to provide both a set of directly usable tools (e.g. normalize-by-median for digital normalization) as well as an experimental framework for developers looking to design new algorithms and methods. It has proven very useful on both of these fronts. The repository is highly watched and starred on GitHub, the developers are very responsive (see more below), and both the senior author's group and other researches seem to be leveraging this framework to build new tools and algorithms.</p><p>The paper itself does a good job of describing the software at a high level, including the overall design and goals. I would have appreciated slightly more detail about the motivation behind the design decisions, and the tradeoffs they entail (e.g. Why have a Python front-end? Why use hand-written binding code rather than a binding generator, like SWIG, that would allow interfaces to other languages as well?). I understand that a comprehensive description is not feasible in a manuscript of this length. It would be very interesting to know, however, the cost paid for using the high-level interface rather than the C++ library directly. When the underlying computation is trivial, simply having to iterate over an enormous number of things in Python could add non-trivial overhead. Despite these desiderata, I find that the paper is generally well written and does a good job of describing what a new user might want to know about khmer, and so I approve of this manuscript.</p><p>Like Daniel, I also downloaded and built the software using the instructions provided in the ReadTheDocs documentation. The process was simple, and worked well, with the exception of a minor glitch running the tests. After debugging the cause of the problem, I posted an issue to the GitHub repository, and received a response in less than a day. I bring this up because, while not an aspect of the paper itself, good developer support is crucial to the long-term survival and utility of a software package — khmer seems to have this.</p><p>This brings me to my final point, about the (currently) controversial authorship policy on this paper, which is ancillary to the quality of the paper (and software) itself. At this point,
<italic>I must reserve judgement</italic> on whether I think the authorship policy adopted by this paper is "good" or "bad" (for science, the community, etc.). Incidentally, this is a dichotomy that does not capture the subtlety or importance of this issue well. In the manuscript, the authors state "We develop khmer on github.com as a community open source project focused on sustainable software development, and encourage contributions of any kind." Thus, contributions to khmer are of a potentially wide variety in character (and also, I believe, not simply related to improving or maintaining the code). Those who contribute to the design, improve the usability, work on documentation, support new and existing users, and develop and propagate best practices are all contributing something valuable to the khmer software "ecosystem". It is unreasonable to expect a piece of software that is ~25k lines of code (and growing) to be actively developed, maintained, and supported by only a small contingent of people, many of whom may be graduate students soon to graduate and move on. Thus, if we are interested in the long-term viability and quality of such software, we must adopt a system of credit that values and recognizes a variety of different types of contribution. On the other hand, I do share the concern that, in the midst of the current authorship system, bestowing that recognition in the form of authorship may have the adverse effect of diminishing the public perception of the very credit one is trying to grant. Perhaps there is a solution
<italic>along</italic> the lines adopted by this paper, or perhaps something drastically different needs to be considered.</p><p>I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body></sub-article><sub-article id="report10513" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.7456.r10513</article-id><title-group><article-title>Referee response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Katz</surname><given-names>Daniel</given-names></name><xref ref-type="aff" rid="r10513a1">1</xref><role>Referee</role></contrib><aff id="r10513a1"><label>1</label>Computation Institute, University of Chicago, Chicago, IL, USA</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>6</day><month>10</month><year>2015</year></pub-date><related-article id="d35e1986" related-article-type="peer-reviewed-article" ext-link-type="doi" xlink:href="10.12688/f1000research.6924.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve</meta-value></custom-meta></custom-meta-group></front-stub><body><p>Regarding the paper, it is a fairly straightforward description of a software package, containing all the things that such a paper should have - a description of the goals, the implemented methods, the hardware and software dependencies (systems on which the software has been tested), some guidance on usage, pointers to the software and documentation, and references.</p><p>Regarding the software, I did download and build the software, which seemed to work, other than a fair number of warnings. I was not able to successfully test the software, however, due to issues in
<ext-link ext-link-type="uri" xlink:href="https://protect-eu.mimecast.com/s/5kZHBM7EDcd">https://khmer.readthedocs.org/en/v2.0/user/install.html#run-the-tests</ext-link> Does this mean I should not approve the article? Or should I ask the authors for help in understanding the error and hold off on submitting this report?</p><p>I would have liked to have chosen "Approved with reservations" for the status of this review, but my reservations are with the F1000 system for this type of paper, not with this specific paper, so in fairness to the authors, given the lack of clarity of what I should be doing as a reviewer for a software paper, I approve this paper based on its quality as a good description of the software, and not on the quality of software (and related documentation) itself.</p><p>I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.</p></body><sub-article id="comment1643" article-type="response"><front-stub><contrib-group><contrib contrib-type="author"><name><surname>Katz</surname><given-names>Daniel S.</given-names></name><aff>University of Chicago, USA</aff></contrib></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>none</p></fn></author-notes><pub-date pub-type="epub"><day>6</day><month>10</month><year>2015</year></pub-date></front-stub><body><p>In addition to my report, regarding software papers in general under F1000, I believe that much more should be required from their reviewers, and what
<bold>is required</bold> should be made clear. Software journals (e.g., Ubiquity Press's Journal of Open Research Software, Elsevier's Software X) have specific statements of what a reviewer should do, which say a lot about the quality of the review. For JORS, this is defined on a web page (
<ext-link ext-link-type="uri" xlink:href="http://openresearchsoftware.metajnl.com/about/editorialPolicies/">http://openresearchsoftware.metajnl.com/about/editorialPolicies/</ext-link>). For Software X, the criteria are not on the web (as far as I know) but are embedded in the review form/process, and are roughly equivalent.</p></body></sub-article></sub-article><sub-article id="report10514" article-type="peer-review"><front-stub><article-id pub-id-type="doi">10.5256/f1000research.7456.r10514</article-id><title-group><article-title>Referee response for version 1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Birney</surname><given-names>Ewan</given-names></name><xref ref-type="aff" rid="r10514a1">1</xref><role>Referee</role></contrib><aff id="r10514a1"><label>1</label>European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK</aff></contrib-group><author-notes><fn fn-type="COI-statement"><p><bold>Competing interests: </bold>No competing interests were disclosed.</p></fn></author-notes><pub-date pub-type="epub"><day>5</day><month>10</month><year>2015</year></pub-date><related-article id="d35e2076" related-article-type="peer-reviewed-article" ext-link-type="doi" xlink:href="10.12688/f1000research.6924.1">Version 1</related-article><custom-meta-group><custom-meta><meta-name>recommendation</meta-name><meta-value>approve-with-reservations</meta-value></custom-meta></custom-meta-group></front-stub><body><p>This is an update of a widely used tool, khmer, which is in broad use in the technical community around de Bruijn graphs and short reads, based on Bloom filters. It is a good update, provides link to the code, and is sensibly written with tests. I have no concern about the scientific aspect of this paper.</p><p>I do find the author inclusion list taking a concept and going to the extreme, and I don't think it is sensible to have an anonymised author (en zyme) on the list, with in effect no way to attribute to a person this. Science's openness in publication is also about attribution. Although I understand Titus' consistency of having all git committers as authors, I think it is sensible to make a distinction of substantial/scientific changes, of which the vast majority of the authors are. Acknowledgements are precisely there to handle these other cases. </p><p>I believe it is uncontroversial to appropriately trim the author list, to use the acknowledgements for anonymous improvement (happens regularly in science) and small details (again, a commonplace practice).</p><p>I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.</p></body></sub-article></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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