The khmer software package: enabling efficient nucleotide sequence analysis

Michael R CrusoeC Titus Brown


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

Associated Software

Jul 3, 2017·Cait SydneyRussell Y. Neches
Sep 21, 2015·Kevin D. MurrayScott Fay

Associated Proceedings Papers

Jul 10, 2019·Alexander LalejiniJory Schossau


May 7, 2016·Bioinformatics·Samuel M NichollsJoshua C Randall
Apr 19, 2016·Algorithms for Molecular Biology : AMB·Guillaume HolleyJens Stoye
Apr 1, 2016·FEMS Microbiology Letters·Bonnie L HurwitzKen Youens-Clark
May 18, 2016·Molecular Biology and Evolution·Tom A WilliamsBryony A P Williams
Aug 7, 2016·Genome Announcements·Hideo DohraShinya Kodani
Jan 13, 2017·PLoS Neglected Tropical Diseases·Daniel SarakaElisabeth Carniel
Jan 8, 2017·Journal of Experimental Botany·Britta M C KümpersJulian M Hibberd
Apr 9, 2017·The Journal of Biological Chemistry·Kristina B MartinezEugene B Chang
Apr 14, 2017·Molecular Ecology Resources·Xin WangManuel Aranda
Apr 14, 2017·Plant Biotechnology Journal·Philipp E BayerDavid Edwards
Oct 27, 2017·Molecular Reproduction and Development·Phillip L DavidsonWilliam E Browne
Dec 1, 2017·Genome Biology and Evolution·Taruna A SchuelkeMatthew D MacManes
Dec 21, 2017·Frontiers in Microbiology·Clara A FuchsmanGabrielle Rocap
Jan 16, 2018·F1000Research·Jessica E MizziBenjamin N Sacks
Aug 28, 2018·PLoS Biology·Jacob A TennessenTia-Lynn Ashman
Sep 2, 2018·Applied and Environmental Microbiology·Amanda BeylefeldCelia Abolnik
Nov 7, 2018·Nature Genetics·International Helminth Genomes Consortium
Jan 25, 2018·BMC Bioinformatics·Thomas C A Hitch, Christopher J Creevey
Jan 9, 2018·Nature Chemical Biology·Tammy M HsuJohn E Dueber
Feb 21, 2019·Proteomics·Christina Maria BredtmannGeorg von Samson-Himmelstjerna
Mar 13, 2019·Journal of Evolutionary Biology·Kevin M HornFrank E Anderson
Mar 24, 2016·Nature Communications·Sesh A SundararamanBeatrice H Hahn
Nov 15, 2016·Journal of Open Research Software·Michael R Crusoe, C Titus Brown
Jun 16, 2019·Veterinary Sciences·Harun AlbayrakManfred Weidmann
Jan 13, 2018·Open Biology·Guy LeonardThomas A Richards


Jan 11, 2008·BMC Bioinformatics·Andreas DöringKnut Reinert
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Aug 9, 2008·Science·Weixing ShenD James Surmeier
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
Aug 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jason PellC Titus Brown
Nov 2, 2012·The Journal of the Royal College of Physicians of Edinburgh·C Brown
Mar 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Adina HoweC Titus Brown

Related Concepts

Computer Software
Severe Acute Respiratory Syndrome
Replication Licensing
Medical Devices
Base Sequence
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