The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]
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 normaliza...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2015-09-01
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| Series: | F1000Research |
| Subjects: | |
| Online Access: | http://f1000research.com/articles/4-900/v1 |
| _version_ | 1818911288675270656 |
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| author | Michael R. Crusoe Hussien F. Alameldin Sherine Awad Elmar Boucher Adam Caldwell Reed Cartwright Amanda Charbonneau Bede Constantinides Greg Edvenson Scott Fay Jacob Fenton Thomas Fenzl Jordan Fish Leonor Garcia-Gutierrez Phillip Garland Jonathan Gluck Iván González Sarah Guermond Jiarong Guo Aditi Gupta Joshua R. Herr Adina Howe Alex Hyer Andreas Härpfer Luiz Irber Rhys Kidd David Lin Justin Lippi Tamer Mansour Pamela McA'Nulty Eric McDonald Jessica Mizzi Kevin D. Murray Joshua R. Nahum Kaben Nanlohy Alexander Johan Nederbragt Humberto Ortiz-Zuazaga Jeramia Ory Jason Pell Charles Pepe-Ranney Zachary N. Russ Erich Schwarz Camille Scott Josiah Seaman Scott Sievert Jared Simpson Connor T. Skennerton James Spencer Ramakrishnan Srinivasan Daniel Standage James A. Stapleton Susan R. Steinman Joe Stein Benjamin Taylor Will Trimble Heather L. Wiencko Michael Wright Brian Wyss Qingpeng Zhang en zyme C. Titus Brown |
| author_facet | Michael R. Crusoe Hussien F. Alameldin Sherine Awad Elmar Boucher Adam Caldwell Reed Cartwright Amanda Charbonneau Bede Constantinides Greg Edvenson Scott Fay Jacob Fenton Thomas Fenzl Jordan Fish Leonor Garcia-Gutierrez Phillip Garland Jonathan Gluck Iván González Sarah Guermond Jiarong Guo Aditi Gupta Joshua R. Herr Adina Howe Alex Hyer Andreas Härpfer Luiz Irber Rhys Kidd David Lin Justin Lippi Tamer Mansour Pamela McA'Nulty Eric McDonald Jessica Mizzi Kevin D. Murray Joshua R. Nahum Kaben Nanlohy Alexander Johan Nederbragt Humberto Ortiz-Zuazaga Jeramia Ory Jason Pell Charles Pepe-Ranney Zachary N. Russ Erich Schwarz Camille Scott Josiah Seaman Scott Sievert Jared Simpson Connor T. Skennerton James Spencer Ramakrishnan Srinivasan Daniel Standage James A. Stapleton Susan R. Steinman Joe Stein Benjamin Taylor Will Trimble Heather L. Wiencko Michael Wright Brian Wyss Qingpeng Zhang en zyme C. Titus Brown |
| author_sort | Michael R. Crusoe |
| collection | DOAJ |
| description | 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/. |
| first_indexed | 2024-12-19T22:56:19Z |
| format | Article |
| id | doaj.art-dc774924b98d40d0bd7efc6c2c5b346c |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-19T22:56:19Z |
| publishDate | 2015-09-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-dc774924b98d40d0bd7efc6c2c5b346c2022-12-21T20:02:38ZengF1000 Research LtdF1000Research2046-14022015-09-01410.12688/f1000research.6924.17456The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]Michael R. Crusoe0Hussien F. Alameldin1Sherine Awad2Elmar Boucher3Adam Caldwell4Reed Cartwright5Amanda Charbonneau6Bede Constantinides7Greg Edvenson8Scott Fay9Jacob Fenton10Thomas Fenzl11Jordan Fish12Leonor Garcia-Gutierrez13Phillip Garland14Jonathan Gluck15Iván González16Sarah Guermond17Jiarong Guo18Aditi Gupta19Joshua R. Herr20Adina Howe21Alex Hyer22Andreas Härpfer23Luiz Irber24Rhys Kidd25David Lin26Justin Lippi27Tamer Mansour28Pamela McA'Nulty29Eric McDonald30Jessica Mizzi31Kevin D. Murray32Joshua R. Nahum33Kaben Nanlohy34Alexander Johan Nederbragt35Humberto Ortiz-Zuazaga36Jeramia Ory37Jason Pell38Charles Pepe-Ranney39Zachary N. Russ40Erich Schwarz41Camille Scott42Josiah Seaman43Scott Sievert44Jared Simpson45Connor T. Skennerton46James Spencer47Ramakrishnan Srinivasan48Daniel Standage49James A. Stapleton50Susan R. Steinman51Joe Stein52Benjamin Taylor53Will Trimble54Heather L. Wiencko55Michael Wright56Brian Wyss57Qingpeng Zhang58en zyme59C. Titus Brown60Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USADepartment of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USAPopulation Health and Reproduction, University of California, Davis, Davis, CA, USADepartment of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USABiology Department, San Jose State University, San Jose, CA, USASchool of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ, USAGenetics, Michigan State University, East Lansing, MI, USAComputational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UKMicron Technology, Seattle, WA, USAInvitae, San Francisco, CA, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USAIndependent Researcher, Munich, GermanyComputer Science and Engineering, Michigan State University, East Lansing, MI, USAMathematics Institute, University of Warwick, Warwick, UKEastlake Data, Seattle, WA, USAGraduate Program, University of Maryland, College Park, MD, USAAthinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USAIndependent Researcher, Seattle, WA, USACenter for Microbial Ecology, Michigan State University, East Lansing, MI, USAMicrobiology and Molecular Genetics, Michigan State University, East Lansing, MI, USAMicrobiology and Molecular Genetics, Michigan State University, East Lansing, MI, USADepartment of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USADepartment of Biology, University of Utah, Salt Lake City, UT, USAConSol* Software GmbH, Munchen, GermanyComputer Science and Engineering, Michigan State University, East Lansing, MI, USAIndependent Researcher, Sydney, AustraliaVerdematics, Fremont, CA, USAIndependent Researcher, San Francisco, CA, USAPopulation Health and Reproduction, University of California, Davis, Davis, CA, USAAddgene, Cambridge, MA, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USABiochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USAARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, ACT, AustraliaBEACON Center, Michigan State University, East Lansing, MI, USAIndependent Researcher, New Orleans, LA, USACentre for Ecological and Evolutionary Synthesis, Dept. of Biosciences, University of Oslo, Oslo, NorwayDepartment of Computer Science, Rio Piedras Campus, University of Puerto Rico, San Juan, Puerto RicoBiochemistry, St. Louis College of Pharmacy, St. Louis, MO, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USACrop and Soil Sciences, Cornell University, Ithaca, NY, USADepartment of Bioengineering, UC Berkeley, Berkeley, CA, USADepartment of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USAData Visualization, Newline Technical Innovations, Windsor, CO, USAElectrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USAOntario Institute for Cancer Research, Toronto, ON, CanadaDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USADept of Physics and Dept of Materials, Imperial College London, London, UKGenetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USADepartment of Biology, Indiana University, Bloomington, IN, USAChemical Engineering & Materials Science, Michigan State University, East Lansing, MIS, USAThe New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USAIndependent Researcher, Providence, RI, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USAMathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USADepartment of Genetics, Smurfit Institute, Trinity College Dublin, Dublin, IrelandComputer Science and Engineering, Michigan State University, East Lansing, MI, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USAComputer Science and Engineering, Michigan State University, East Lansing, MI, USAIndependent Researcher, Boston, MA, USAMicrobiology and Molecular Genetics, Michigan State University, East Lansing, MI, USAThe 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/.http://f1000research.com/articles/4-900/v1Bioinformatics |
| spellingShingle | Michael R. Crusoe Hussien F. Alameldin Sherine Awad Elmar Boucher Adam Caldwell Reed Cartwright Amanda Charbonneau Bede Constantinides Greg Edvenson Scott Fay Jacob Fenton Thomas Fenzl Jordan Fish Leonor Garcia-Gutierrez Phillip Garland Jonathan Gluck Iván González Sarah Guermond Jiarong Guo Aditi Gupta Joshua R. Herr Adina Howe Alex Hyer Andreas Härpfer Luiz Irber Rhys Kidd David Lin Justin Lippi Tamer Mansour Pamela McA'Nulty Eric McDonald Jessica Mizzi Kevin D. Murray Joshua R. Nahum Kaben Nanlohy Alexander Johan Nederbragt Humberto Ortiz-Zuazaga Jeramia Ory Jason Pell Charles Pepe-Ranney Zachary N. Russ Erich Schwarz Camille Scott Josiah Seaman Scott Sievert Jared Simpson Connor T. Skennerton James Spencer Ramakrishnan Srinivasan Daniel Standage James A. Stapleton Susan R. Steinman Joe Stein Benjamin Taylor Will Trimble Heather L. Wiencko Michael Wright Brian Wyss Qingpeng Zhang en zyme C. Titus Brown The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] F1000Research Bioinformatics |
| title | The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] |
| title_full | The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] |
| title_fullStr | The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] |
| title_full_unstemmed | The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] |
| title_short | The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations] |
| title_sort | khmer software package enabling efficient nucleotide sequence analysis version 1 referees 2 approved 1 approved with reservations |
| topic | Bioinformatics |
| url | http://f1000research.com/articles/4-900/v1 |
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