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KMC | Disk-based k-mer counting on a PC

A utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. K-mer counting is important for many bioinformatics applications, e.g., developing de Bruijn graph assemblers. KMC 2 counts the 28-mers of a human reads collection with 44-fold coverage (106GB of compressed size) in about 20 minutes, on a 6-core Intel i7 PC with an SSD.

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KMC forum

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KMC classification

KMC specifications

Unique identifier:
OMICS_02095
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Version:
2.0
Maintained:
Yes
Name:
K-Mer Counter
Interface:
Command line interface
Operating system:
Unix/Linux, Windows
Computer skills:
Advanced
Stability:
Stable

KMC distribution

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KMC support

Maintainer

  • Sebastian Deorowicz <>

Credits

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Publications

Institution(s)

Institute of Informatics, Silesian University of Technology, Gliwice, Poland

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