The khmer software for advanced biological sequencing data analysis

What is khmer?

The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. You can read more about khmer in our software paper.

khmer is free and open source software.

To install khmer, you will need a Linux or Mac computer, together with Python 2.7 or Python 3.x. See our installation docs for detailed instructions.

To use khmer, you will generally need to work at the UNIX command line. See our command line documentation.

We have additional documentation in several places, including protocols for metagenome and mRNAseq assembly and recipes for several common research tasks. You might also be interested in papers using or citing khmer.

To get help, please follow this guide.

We welcome contributions to the khmer project! We are friendly and supportive of new contributors, and have a code of conduct. Please see our docs on getting started on khmer development.


Authors:Daniel Standage, Hussien F. Alameldin, Ali Aliyari, Sherine Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Lisa Cohen, Bede Constantinides, Michael R. Crusoe, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia- Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Tim Head, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Shannon EK Joslin, Rhys Kidd, Nicole Kingsley, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Russell Neches, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Ryan Shean, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, James A. Stapleton, Joe Stein, Sascha Steinbiss, Susan R Steinman, Cait Sydney, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme, C. Titus Brown

There are two mailing lists dedicated to khmer, an announcements-only list and a discussion list. To search their archives and sign-up for them, please visit the following URLs:

The archives for the khmer mailing list are available at:

khmer development was initially supported by AFRI Competitive Grant no. 2010-65205-20361 from the USDA NIFA, and is now funded by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG007513 through May 2016, both to C. Titus Brown. More recently, we have received support from the Gordon and Betty Moore Foundation under Award number GBMF4551.

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