Simka

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.

Reference

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

Poster

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)
Download
linuxlogo Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
Download

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

License

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

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