KMC 3: counting and manipulating k-mer statistics

Abstract

Summary: Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems. Availability and implementation: Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc . Contact: sebastian.deorowicz@polsl.pl. Supplementary information: Supplementary data are available at Bioinformatics online.