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/.
Original language | English (US) |
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Article number | 900 |
Journal | F1000Research |
Volume | 4 |
DOIs | |
State | Published - 2015 |
Keywords
- Bioinformatics
- Dna sequencing analysis
- K-mer
- Khmer
- Kmer
- Low-memory
- Online
- Streaming
ASJC Scopus subject areas
- Biochemistry, Genetics and Molecular Biology(all)
- Immunology and Microbiology(all)
- Pharmacology, Toxicology and Pharmaceutics(all)
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The khmer project v2.0
Brown, C. T. (Contributor), Crusoe, M. R. (Contributor), Alameldin, H. F. (Contributor), Awad, S. (Contributor), Boucher, E. (Contributor), Caldwell, A. (Contributor), Cartwright, R. (Contributor), Charbonneau, A. (Contributor), Constantinides, B. (Contributor), Edvenson, G. (Contributor), Fay, S. (Contributor), Fenton, J. (Contributor), Fenzl, T. (Contributor), Fish, J. (Contributor), Garcia-Gutierrez, L. (Contributor), Garland, P. (Contributor), Gluck, J. (Contributor), González, I. (Contributor), Guermond, S. (Contributor), Guo, J. (Contributor), Gupta, A. (Contributor), Herr, J. R. (Contributor), Howe, A. (Contributor), Hyer, A. (Contributor), Härpfer, A. (Contributor), Irber, L. (Contributor), Kidd, R. (Contributor), Lin, D. (Contributor), Lippi, J. (Contributor), Mansour, T. (Contributor), McA'Nulty, P. (Contributor), McDonald, E. (Contributor), Mizzi, J. (Contributor), Murray, K. D. (Contributor), Nahum, J. R. (Contributor), Nanlohy, K. (Contributor), Nederbragt, A. J. (Contributor), Ortiz-Zuazaga, H. (Contributor), Ory, J. (Contributor), Pell, J. (Contributor), Pepe-Ranney, C. (Contributor), Russ, Z. N. (Contributor), Schwarz, E. (Contributor), Scott, C. (Contributor), Seaman, J. (Contributor), Sievert, S. (Contributor), Simpson, J. (Contributor), Skennerton, C. T. (Contributor), Spencer, J. (Contributor), Srinivasan, R. (Contributor), Standage, D. (Contributor), Stapleton, J. A. (Contributor), Steinman, S. R. (Contributor), Stein, J. (Contributor), Taylor, B. (Contributor), Trimble, W. (Contributor), Wiencko, H. L. (Contributor), Wright, M. (Contributor), Wyss, B. (Contributor), Zhang, Q. (Contributor) & Zyme, E. (Contributor), Zenodo, 2015
DOI: 10.5281/zenodo.31258, https://zenodo.org/record/31258
Dataset
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The khmer project v2.0
Wyss, B. (Contributor), Zhang, Q. (Contributor), Nanlohy, K. (Contributor), Scott, C. (Contributor), Taylor, B. (Contributor), Pell, J. (Contributor), Mansour, T. (Contributor), Trimble, W. (Contributor), Wright, M. (Contributor), Seaman, J. (Contributor), Irber, L. (Contributor), Ortiz-Zuazaga, H. (Contributor), Boucher, E. (Contributor), McA'Nulty, P. (Contributor), Gupta, A. (Contributor), Standage, D. (Contributor), Härpfer, A. (Contributor), Spencer, J. (Contributor), Srinivasan, R. (Contributor), Constantinides, B. (Contributor), Kidd, R. (Contributor), Charbonneau, A. (Contributor), Crusoe, M. R. (Contributor), Lin, D. (Contributor), Guermond, S. (Contributor), Mizzi, J. (Contributor), Pepe-Ranney, C. (Contributor), Garland, P. (Contributor), Sievert, S. (Contributor), Caldwell, A. (Contributor), Ory, J. (Contributor), Schwarz, E. (Contributor), Stapleton, J. A. (Contributor), Nahum, J. R. (Contributor), Simpson, J. (Contributor), McDonald, E. (Contributor), Hyer, A. (Contributor), Edvenson, G. (Contributor), Murray, K. D. (Contributor), González, I. (Contributor), Howe, A. (Contributor), Steinman, S. R. (Contributor), Awad, S. (Contributor), Herr, J. R. (Contributor), Cartwright, R. (Contributor), Lippi, J. (Contributor), Nederbragt, A. J. (Contributor), Brown, C. T. (Contributor), Stein, J. (Contributor), Fish, J. (Contributor), Alameldin, H. F. (Contributor), Fenzl, T. (Contributor), Skennerton, C. T. (Contributor), Gluck, J. (Contributor), Russ, Z. N. (Contributor), Wiencko, H. L. (Contributor), Zyme, E. (Contributor), Guo, J. (Contributor), Garcia-Gutierrez, L. (Contributor), Fay, S. (Contributor) & Fenton, J. (Contributor), Zenodo, Sep 8 2015
DOI: 10.5281/zenodo.31258, https://zenodo.org/record/31258
Dataset