Agricultural and Biosystems Engineering Publications
Campus Units
Agricultural and Biosystems Engineering, Bioinformatics and Computational Biology
Document Type
Article
Publication Version
Published Version
Publication Date
9-25-2015
Journal or Book Title
F1000Research
Volume
4
First Page
900
DOI
10.12688/f1000research.6924.1
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/.
Access
Open
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright Owner
Crusoe MR et al
Copyright Date
2015
Language
en
File Format
application/pdf
Recommended Citation
Crusoe, Michael R.; Alameldin, Hussein 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 C.; Hyer, Alex; Härpfer, Andreas; Irber, Luiz; Kidd, Rhys; Lin, David; Lippi, Justin; Mansour, Tamer; McA'Nulty, Pamela; McDonald, Erin; 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 S.; Stapleton, James A.; Steinman, Susan R.; Stein, Joe; Taylor, Benjamin; Tremble, Will; Wiencko, Heather L.; Wright, Michael; Wyss, Brian; Zhang, Qingpeng; zyme, en; and Brown, C. Titus, "The khmer software package: enabling efficient nucleotide sequence analysis" (2015). Agricultural and Biosystems Engineering Publications. 713.
https://lib.dr.iastate.edu/abe_eng_pubs/713
Included in
Agriculture Commons, Bioresource and Agricultural Engineering Commons, Computational Biology Commons, Numerical Analysis and Scientific Computing Commons
Comments
This article is from F1000Research 2015, 4:900 (doi:10.12688/f1000research.6924.1). Posted with permission.