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khmer website  

Khmer - python scripts for k-mer counting, filtering and graph traversal.

There's a khmer mailing list at that you can use to get help with khmer. To sign up, email '' to subscribe; then send your question/comment there.


khmer is *pre-publication* and *research* software, so please keep in mind that (a) the code may have undiscovered bugs in it, (b) you should cite us, and (c) you should get in touch if you need to cite us, as we are writing up the project.

Available scripts:,,,,,,,,,,,,,,,,

Use "import khmer" in your script or in an interactive python session.

Required Modules

modules documentation


  • khmer

System Variables

  • HPC_{{#uppercase:khmer}}_DIR


If you use the khmer software, you must cite:

Crusoe et al., The khmer software package: enabling efficient sequence analysis. 2014. doi: 10.6084/m9.figshare.979190

If you use any of khmer's published scientific methods, you should *also* cite the relevant paper(s), as directed below.

  • Graph partitioning and/or compressible graph representation
The,,,, and scripts are part of the compressible graph representation and partitioning algorithms described in:
Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT
Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7
doi: 10.1073/pnas.1121464109
PMID: 22847406
  • Digital normalization
The and scripts are part of the digital normalization algorithm, described in:
A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data
Brown CT, Howe AC, Zhang Q, Pyrkosz AB, Brom TH
arXiv:1203.4802 [q-bio.GN]
  • K-mer counting
The,, and scripts implement the probabilistic k-mer counting described in:
These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure
Zhang Q, Pell J, Canino-Koning R, Howe AC, Brown CT.
arXiv:1309.2975 [q-bio.GN]