KMC 3: counting and manipulating k -mer statistics

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.

• NC
  Narodowe Centrum Nauki

  Award: DEC-2015/17/B/ST6/01890
• SU
  Silesian University of Technology

  Awards: BKM507/RAU2/2016, POIG.02.03.01-24-099/13