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:
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MacOS-X 10.9 or above. (Intel 64bit processors) |
Download |
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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
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Simka tool is fully written in C++. | Download |
License
Simka binaries and source code are covered by the Affero GPL version 3 license.
