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
Simka is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:
|MacOS-X 10.9 or above.
(Intel 64bit processors)
|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.
|Simka tool is fully written in C++.
Simka binaries and source code are covered by the Affero GPL version 3 license.