Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.


Benoit G, Peterlongo P, Mariadassou M, Drezen E, Schbath S, Lavenier D, Lemaitre C. (2016) Multiple comparative metagenomics using multiset k-mer counting. PeerJ Computer Science 2:e94


G. Benoit, P. Peterlongo, D. Lavenier, C. Lemaitre. (2015) Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets. Hal-Inria

Ready-to-use executable

Simka is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:

maclogo MacOS-X 10.9 or above.
(Intel 64bit processors)
linuxlogo Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)

For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.

Source Code

cpp-logo Simka tool is fully written in C++. Download


Simka binaries and source code are covered by the Affero GPL version 3 license.

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