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The khmer software package: enabling efficient nucleotide sequence analysis.
Crusoe, Michael R; Alameldin, Hussien F; Awad, Sherine; Boucher, Elmar; Caldwell, Adam; Cartwright, Reed; Charbonneau, Amanda; Constantinides, Bede; Edvenson, Greg; Fay, Scott; Fenton, Jacob; Fenzl, Thomas; Fish, Jordan; Garcia-Gutierrez, Leonor; Garland, Phillip; Gluck, Jonathan; González, Iván; Guermond, Sarah; Guo, Jiarong; Gupta, Aditi; Herr, Joshua R; Howe, Adina; Hyer, Alex; Härpfer, Andreas; Irber, Luiz; Kidd, Rhys; Lin, David; Lippi, Justin; Mansour, Tamer; McA'Nulty, Pamela; McDonald, Eric; Mizzi, Jessica; Murray, Kevin D; Nahum, Joshua R; Nanlohy, Kaben; Nederbragt, Alexander Johan; Ortiz-Zuazaga, Humberto; Ory, Jeramia; Pell, Jason; Pepe-Ranney, Charles; Russ, Zachary N; Schwarz, Erich; Scott, Camille; Seaman, Josiah; Sievert, Scott; Simpson, Jared; Skennerton, Connor T; Spencer, James; Srinivasan, Ramakrishnan; Standage, Daniel.
Afiliação
  • Crusoe MR; Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
  • Alameldin HF; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
  • Awad S; Population Health and Reproduction, University of California, Davis, Davis, CA, USA.
  • Boucher E; Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
  • Caldwell A; Biology Department, San Jose State University, San Jose, CA, USA.
  • Cartwright R; School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
  • Charbonneau A; Genetics, Michigan State University, East Lansing, MI, USA.
  • Constantinides B; Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
  • Edvenson G; Micron Technology, Seattle, WA, USA.
  • Fay S; Invitae, San Francisco, CA, USA.
  • Fenton J; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Fenzl T; Independent Researcher, Munich, Germany.
  • Fish J; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Garcia-Gutierrez L; Mathematics Institute, University of Warwick, Warwick, UK.
  • Garland P; Eastlake Data, Seattle, WA, USA.
  • Gluck J; Graduate Program, University of Maryland, College Park, MD, USA.
  • González I; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA.
  • Guermond S; Independent Researcher, Seattle, WA, USA.
  • Guo J; Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
  • Gupta A; Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
  • Herr JR; Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
  • Howe A; Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.
  • Hyer A; Department of Biology, University of Utah, Salt Lake City, UT, USA.
  • Härpfer A; ConSol Software GmbH, Munchen, Germany.
  • Irber L; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Kidd R; Independent Researcher, Sydney, Australia.
  • Lin D; Verdematics, Fremont, CA, USA.
  • Lippi J; Independent Researcher, San Francisco, CA, USA.
  • Mansour T; Population Health and Reproduction, University of California, Davis, Davis, CA, USA ; Clinical Pathology, Mansoura University, Mansoura, Egypt.
  • McA'Nulty P; Addgene, Cambridge, MA, USA.
  • McDonald E; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Mizzi J; Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
  • Murray KD; ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, Australia.
  • Nahum JR; BEACON Center, Michigan State University, East Lansing, MI, USA.
  • Nanlohy K; Independent Researcher, New Orleans, LA, USA.
  • Nederbragt AJ; Centre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, Norway.
  • Ortiz-Zuazaga H; Department of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto Rico.
  • Ory J; Biochemistry, St. Louis College of Pharmacy, St. Louis, MO, USA.
  • Pell J; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Pepe-Ranney C; Crop and Soil Sciences, Cornell University, Ithaca, NY, USA.
  • Russ ZN; Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
  • Schwarz E; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
  • Scott C; Computer Science and Engineering, Michigan State University, East Lansing, MI, USA.
  • Seaman J; Data Visualization, Newline Technical Innovations, Windsor, CO, USA.
  • Sievert S; Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA.
  • Simpson J; Ontario Institute for Cancer Research, Toronto, ON, Canada ; Computer Science, University of Toronto, Toronto, ON, Canada.
  • Skennerton CT; Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.
  • Spencer J; Dept of Physics and Dept of Materials, Imperial College London, London, UK.
  • Srinivasan R; Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Standage D; Department of Biology, Indiana University, Bloomington, IN, USA ; Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA.
F1000Res ; 4: 900, 2015.
Article em En | MEDLINE | ID: mdl-26535114
ABSTRACT
The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https//github.com/dib-lab/khmer/.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: F1000Res Ano de publicação: 2015 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Idioma: En Revista: F1000Res Ano de publicação: 2015 Tipo de documento: Article País de afiliação: Estados Unidos