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Section: New Software and Platforms
Simka
Keywords: Comparative metagenomics - K-mer - Distance - Ecology
Functional Description: Simka is a comparative metagenomics method dedicated to NGS datasets. It computes a large collection of distances classically used in ecology to compare communities by approximating species counts by k-mer counts. The method scales to a large number of datasets thanks to an efficient and parallel kmer-counting strategy that processes all datasets simultaneoulsy. SimkaMin is distributed also with Simka. SimkaMin is a faster and more resource-frugal version of Simka. It outputs approximate (but very similar) results by subsampling the kmer space.
Release Functional Description: Since release version 1.5.0, SimkaMin is distributed alongside Simka. SimkaMin is also a de novo comparative metagenomics tool. It is a faster and more resource-frugal version of Simka. It outputs approximate (but very similar) results as Simka by subsampling the kmer space. With this strategy, and with default parameters, SimkaMin is an order of magnitude faster, uses 10 times less memory and 70 times less disk than Simka.