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khmer website  

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

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

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

Required Modules

modules documentation


  • khmer

System Variables



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]


  • Validated 4/5/2018