simkamin

Description

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.

The difference with Simka stands in the fact that SimkaMin outputs approximate (but very similar) results 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.

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Homepage

https://github.com/GATB/simka

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