The khmer software package: enabling efficient nucleotide sequence analysis.
Identifieur interne : 001404 ( PubMed/Curation ); précédent : 001403; suivant : 001405The 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 [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 https://github.com/dib-lab/khmer/.
DOI: 10.12688/f1000research.6924.1
PubMed: 26535114
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Steinman</name><affiliation wicri:level="1"><nlm:affiliation>The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.</nlm:affiliation><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:affiliation>Independent Researcher, Providence, RI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.</nlm:affiliation><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:affiliation>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Independent Researcher, Boston, MA, USA.</nlm:affiliation><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:affiliation>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.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>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</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26535114</idno><idno type="pmid">26535114</idno><idno type="doi">10.12688/f1000research.6924.1</idno><idno type="wicri:Area/PubMed/Corpus">001404</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001404</idno><idno type="wicri:Area/PubMed/Curation">001404</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001404</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">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:affiliation>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Population Health and Reproduction, University of California, Davis, Davis, CA, USA.</nlm:affiliation><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:affiliation>Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.</nlm:affiliation><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:affiliation>Biology Department, San Jose State University, San Jose, CA, USA.</nlm:affiliation><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:affiliation>School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.</nlm:affiliation><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:affiliation>Genetics, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.</nlm:affiliation><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:affiliation>Micron Technology, Seattle, WA, USA.</nlm:affiliation><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:affiliation>Invitae, San Francisco, CA, USA.</nlm:affiliation><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 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USA.</nlm:affiliation><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:affiliation>Mathematics Institute, University of Warwick, Warwick, UK.</nlm:affiliation><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:affiliation>Eastlake Data, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Eastlake Data, Seattle, 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Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.</nlm:affiliation><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:affiliation>Independent Researcher, Seattle, WA, USA.</nlm:affiliation><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:affiliation>Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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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Clinical Pathology, Mansoura University, Mansoura, Egypt.</nlm:affiliation><country xml:lang="fr">Égypte</country><wicri:regionArea>Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; 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:affiliation>Addgene, Cambridge, MA, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.</nlm:affiliation><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:affiliation>BEACON Center, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Independent Researcher, New Orleans, LA, USA.</nlm:affiliation><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:affiliation>Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.</nlm:affiliation><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:affiliation>Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.</nlm:affiliation><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:affiliation>Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.</nlm:affiliation><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:affiliation>Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.</nlm:affiliation><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:affiliation>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Data Visualization, Newline Technical Innovations, Windsor, CO, USA.</nlm:affiliation><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:affiliation>Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.</nlm:affiliation><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:affiliation>Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Ontario Institute for Cancer Research, Toronto, ON, Canada ; 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:affiliation>Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.</nlm:affiliation><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:affiliation>Dept of Physics and Dept of Materials, Imperial College London, London, UK.</nlm:affiliation><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:affiliation>Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.</nlm:affiliation><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:affiliation>Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Indiana University, Bloomington, IN, USA ; 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:affiliation>Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA.</nlm:affiliation><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:affiliation>The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.</nlm:affiliation><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:affiliation>Independent Researcher, Providence, RI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.</nlm:affiliation><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:affiliation>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</nlm:affiliation><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:affiliation>Independent Researcher, Boston, MA, USA.</nlm:affiliation><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:affiliation>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.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>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</wicri:regionArea></affiliation></author></analytic><series><title level="j">F1000Research</title><idno type="ISSN">2046-1402</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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/. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26535114</PMID><DateCompleted><Year>2015</Year><Month>11</Month><Day>04</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2046-1402</ISSN><JournalIssue CitedMedium="Print"><Volume>4</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>F1000Research</Title><ISOAbbreviation>F1000Res</ISOAbbreviation></Journal><ArticleTitle>The khmer software package: enabling efficient nucleotide sequence analysis.</ArticleTitle><Pagination><MedlinePgn>900</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.12688/f1000research.6924.1</ELocationID><Abstract><AbstractText>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/. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Crusoe</LastName><ForeName>Michael R</ForeName><Initials>MR</Initials><AffiliationInfo><Affiliation>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Alameldin</LastName><ForeName>Hussien F</ForeName><Initials>HF</Initials><AffiliationInfo><Affiliation>Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Awad</LastName><ForeName>Sherine</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Population Health and Reproduction, University of California, Davis, Davis, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Boucher</LastName><ForeName>Elmar</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Caldwell</LastName><ForeName>Adam</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Biology Department, San Jose State University, San Jose, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cartwright</LastName><ForeName>Reed</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Charbonneau</LastName><ForeName>Amanda</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Genetics, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Constantinides</LastName><ForeName>Bede</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Edvenson</LastName><ForeName>Greg</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Micron Technology, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fay</LastName><ForeName>Scott</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Invitae, San Francisco, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fenton</LastName><ForeName>Jacob</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fenzl</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Independent Researcher, Munich, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fish</LastName><ForeName>Jordan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garcia-Gutierrez</LastName><ForeName>Leonor</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Mathematics Institute, University of Warwick, Warwick, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Garland</LastName><ForeName>Phillip</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Eastlake Data, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gluck</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Graduate Program, University of Maryland, College Park, MD, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>González</LastName><ForeName>Iván</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guermond</LastName><ForeName>Sarah</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Independent Researcher, Seattle, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Jiarong</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gupta</LastName><ForeName>Aditi</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herr</LastName><ForeName>Joshua R</ForeName><Initials>JR</Initials><AffiliationInfo><Affiliation>Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Howe</LastName><ForeName>Adina</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hyer</LastName><ForeName>Alex</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biology, University of Utah, Salt Lake City, UT, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Härpfer</LastName><ForeName>Andreas</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>ConSol Software GmbH, Munchen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Irber</LastName><ForeName>Luiz</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kidd</LastName><ForeName>Rhys</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Independent Researcher, Sydney, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Verdematics, Fremont, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lippi</LastName><ForeName>Justin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Independent Researcher, San Francisco, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mansour</LastName><ForeName>Tamer</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Clinical Pathology, Mansoura University, Mansoura, Egypt.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McA'Nulty</LastName><ForeName>Pamela</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Addgene, Cambridge, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>McDonald</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mizzi</LastName><ForeName>Jessica</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Murray</LastName><ForeName>Kevin D</ForeName><Initials>KD</Initials><AffiliationInfo><Affiliation>ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nahum</LastName><ForeName>Joshua R</ForeName><Initials>JR</Initials><AffiliationInfo><Affiliation>BEACON Center, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nanlohy</LastName><ForeName>Kaben</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Independent Researcher, New Orleans, LA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nederbragt</LastName><ForeName>Alexander Johan</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ortiz-Zuazaga</LastName><ForeName>Humberto</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ory</LastName><ForeName>Jeramia</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pell</LastName><ForeName>Jason</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pepe-Ranney</LastName><ForeName>Charles</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Russ</LastName><ForeName>Zachary N</ForeName><Initials>ZN</Initials><AffiliationInfo><Affiliation>Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schwarz</LastName><ForeName>Erich</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scott</LastName><ForeName>Camille</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seaman</LastName><ForeName>Josiah</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Data Visualization, Newline Technical Innovations, Windsor, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sievert</LastName><ForeName>Scott</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Simpson</LastName><ForeName>Jared</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Skennerton</LastName><ForeName>Connor T</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Spencer</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Dept of Physics and Dept of Materials, Imperial College London, London, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Srinivasan</LastName><ForeName>Ramakrishnan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Standage</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stapleton</LastName><ForeName>James A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Chemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Steinman</LastName><ForeName>Susan R</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>The New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stein</LastName><ForeName>Joe</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Independent Researcher, Providence, RI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Trimble</LastName><ForeName>Will</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wiencko</LastName><ForeName>Heather L</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>Department of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, Ireland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wright</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wyss</LastName><ForeName>Brian</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Qingpeng</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zyme</LastName><ForeName>En</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Independent Researcher, Boston, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>C Titus</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>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.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 HG007513</GrantID><Acronym>HG</Acronym><Agency>NHGRI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>09</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>F1000Res</MedlineTA><NlmUniqueID>101594320</NlmUniqueID><ISSNLinking>2046-1402</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">bioinformatics</Keyword><Keyword MajorTopicYN="N">dna sequencing analysis</Keyword><Keyword MajorTopicYN="N">k-mer</Keyword><Keyword MajorTopicYN="N">khmer</Keyword><Keyword MajorTopicYN="N">kmer</Keyword><Keyword MajorTopicYN="N">low-memory</Keyword><Keyword MajorTopicYN="N">online</Keyword><Keyword MajorTopicYN="N">streaming</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>09</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>11</Month><Day>5</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26535114</ArticleId><ArticleId IdType="doi">10.12688/f1000research.6924.1</ArticleId><ArticleId IdType="pmc">PMC4608353</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genome Res. 2008 May;18(5):821-9</Citation><ArticleIdList><ArticleId IdType="pubmed">18349386</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2013 Aug;8(8):1494-512</Citation><ArticleIdList><ArticleId IdType="pubmed">23845962</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2008 Jan 09;9:11</Citation><ArticleIdList><ArticleId IdType="pubmed">18184432</ArticleId></ArticleIdList></Reference><Reference><Citation>J Open Res Softw. 2016;4(1):</Citation><ArticleIdList><ArticleId IdType="pubmed">27840675</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2014 Jul 25;9(7):e101271</Citation><ArticleIdList><ArticleId IdType="pubmed">25062443</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4904-9</Citation><ArticleIdList><ArticleId IdType="pubmed">24632729</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Biol. 2012 May;19(5):455-77</Citation><ArticleIdList><ArticleId IdType="pubmed">22506599</ArticleId></ArticleIdList></Reference><Reference><Citation>J Open Res Softw. 2016;4(1):</Citation><ArticleIdList><ArticleId IdType="pubmed">27942385</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7</Citation><ArticleIdList><ArticleId IdType="pubmed">22847406</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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