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

Sebastian Deorowicz; Marek Kokot; Szymon Grabowski; Agnieszka Debudaj-Grabysz

doi:10.1093/bioinformatics/btv022

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arXiv · 1407.1507

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

Sebastian Deorowicz·Marek Kokot·Szymon Grabowski·Agnieszka Debudaj-Grabysz

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Abstract

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 12\,GB (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 (106\,GB 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

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Sebastian Deorowicz, Marek Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz. 2014-07-06. KMC 2: Fast and resource-frugal $k$-mer counting. https://doi.org/10.1093/bioinformatics%2Fbtv022

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