KMC 2: Fast and resource-frugal k-mer counting

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Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory. Results: We present a novel method for k-mer counting, on large datasets at least twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12GB (or less) of RAM memory. Our disk-based method bears some resemblance to MSPKmerCounter, yet replacing the original minimizers with signatures (a carefully selected subset of all minimizers) and using (k, x)-mers allows to significantly reduce the I/O, and a highly parallel overall architecture allows to achieve unprecedented processing speeds. For example, KMC 2 allows to count the 28-mers of a human reads collection with 44-fold coverage (106GB of compressed size) in about 20 minutes, on a 6-core Intel i7 PC with an SSD. Availability: KMC 2 is freely available at http://sun.aei.polsl.pl/kmc. Contact: sebastian.deorowicz@polsl.pl