The khmer software package: enabling efficient nucleotide sequence analysis

  title={The khmer software package: enabling efficient nucleotide sequence analysis},
  author={Michael R. Crusoe and Hussien F. Alameldin and Sherine Awad and Elmar Boucher and Adam Caldwell and Reed A. Cartwright and Amanda L Charbonneau and Bede Constantinides and Greg Edvenson and Scott Fay and Jacob Fenton and Thomas Fenzl and Jordan A. Fish and Leonor Garcia-Gutierrez and Phillip Garland and Jonathan Gluck and Iv{\'a}n Gonz{\'a}lez and Sarah M. Guermond and Jiarong Guo and Aditi Gupta and Joshua R. Herr and Adina Howe and Alex J. Hyer and Andreas H{\"a}rpfer and Luiz C. Irber and R. C. Kidd and David Lin and Justin Lippi and Tamer A. Mansour and Pamela McA'Nulty and Eric McDonald and Jessica Mizzi and Kevin D. Murray and Joshua R. Nahum and Kaben Nanlohy and Alexander J. Nederbragt and Humberto Ortiz-Zuazaga and Jeramia Ory and Jason Pell and Charles Pepe-Ranney and Zachary N Russ and Erich M. Schwarz and Camille Scott and Josiah D. Seaman and Scott Sievert and Jared T. Simpson and Connor T Skennerton and J. S. Spencer and Ramakrishnan R Srinivasan and Daniel S. Standage and James A. Stapleton and Susan R. Steinman and Joe Stein and Benjamin R. Taylor and Will Trimble and Heather L. Wiencko and M. Wright and Brian Wyss and Qingpeng Zhang and en zyme and C. Titus Brown and Rob Patro and Daniel S Katz and Ewan Birney},
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 
Highly Cited
This paper has 443 citations. REVIEW CITATIONS
Recent Discussions
This paper has been referenced on Twitter 123 times over the past 90 days. VIEW TWEETS

From This Paper

Topics from this paper.


Publications citing this paper.
Showing 1-10 of 92 extracted citations

444 Citations

Citations per Year
Semantic Scholar estimates that this publication has 444 citations based on the available data.

See our FAQ for additional information.


Publications referenced by this paper.
Showing 1-10 of 15 references

Semantic versioning 2.0.0

  • T Preston-Werner
  • [Online; accessed 3-August2015]. Reference Source
  • 2015

Evaluating a lightweight transcriptome assembly pipeline on two closely related ascidian species

  • EK Lowe, BJ Swalla, CT Brown
  • PeerJ Preprints
  • 2014

Similar Papers

Loading similar papers…