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The khmer software package: enabling efficient nucleotide sequence analysis
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...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
F1000Research
2015
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608353/ https://www.ncbi.nlm.nih.gov/pubmed/26535114 http://dx.doi.org/10.12688/f1000research.6924.1 |
| _version_ | 1782395660006326272 |
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| author | 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 Stapleton, James A. Steinman, Susan R. Stein, Joe Taylor, Benjamin Trimble, Will Wiencko, Heather L. Wright, Michael Wyss, Brian Zhang, Qingpeng zyme, en Brown, C. Titus |
| author_facet | 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 Stapleton, James A. Steinman, Susan R. Stein, Joe Taylor, Benjamin Trimble, Will Wiencko, Heather L. Wright, Michael Wyss, Brian Zhang, Qingpeng zyme, en Brown, C. Titus |
| author_sort | Crusoe, Michael R. |
| collection | PubMed |
| 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/. |
| format | Online Article Text |
| id | pubmed-4608353 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2015 |
| publisher | F1000Research |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-46083532015-11-02 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 Stapleton, James A. Steinman, Susan R. Stein, Joe Taylor, Benjamin Trimble, Will Wiencko, Heather L. Wright, Michael Wyss, Brian Zhang, Qingpeng zyme, en Brown, C. Titus F1000Res Software Tool Article 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/. F1000Research 2015-09-25 /pmc/articles/PMC4608353/ /pubmed/26535114 http://dx.doi.org/10.12688/f1000research.6924.1 Text en Copyright: © 2015 Crusoe MR et al. http://creativecommons.org/licenses/by/4.0/ 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. |
| spellingShingle | Software Tool Article 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 Stapleton, James A. Steinman, Susan R. Stein, Joe Taylor, Benjamin Trimble, Will Wiencko, Heather L. Wright, Michael Wyss, Brian Zhang, Qingpeng zyme, en Brown, C. Titus The khmer software package: enabling efficient nucleotide sequence analysis |
| title | The khmer software package: enabling efficient nucleotide sequence analysis |
| title_full | The khmer software package: enabling efficient nucleotide sequence analysis |
| title_fullStr | The khmer software package: enabling efficient nucleotide sequence analysis |
| title_full_unstemmed | The khmer software package: enabling efficient nucleotide sequence analysis |
| title_short | The khmer software package: enabling efficient nucleotide sequence analysis |
| title_sort | khmer software package: enabling efficient nucleotide sequence analysis |
| topic | Software Tool Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608353/ https://www.ncbi.nlm.nih.gov/pubmed/26535114 http://dx.doi.org/10.12688/f1000research.6924.1 |
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