Gerbil: a fast and memory-efficient k-mer counter with GPU-support

• Main Authors: Marius Erbert, Steffen Rechner, Matthias Müller-Hannemann
• Format: Article
• Language: English
• Published: BMC 2017-03-01
• Series: Algorithms for Molecular Biology
• Subjects: k-mer counting; de novo assembly; Genome sequences; GPU computing; Algorithm engineering
• Online Access: http://link.springer.com/article/10.1186/s13015-017-0097-9

Abstract Background A basic task in bioinformatics is the counting of k-mers in genome sequences. Existing k-mer counting tools are most often optimized for small k < 32 and suffer from excessive memory resource consumption or degrading performance for large k. However, given the technology trend towards long reads of next-generation sequencers, support for large k becomes increasingly important. Results We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k ≥ 32. Our software is the result of an intensive process of algorithm engineering. It implements a two-step approach. In the first step, genome reads are loaded from disk and redistributed to temporary files. In a second step, the k-mers of each temporary file are counted via a hash table approach. In addition to its basic functionality, Gerbil can optionally use GPUs to accelerate the counting step. In a set of experiments with real-world genome data sets, we show that Gerbil is able to efficiently support both small and large k. Conclusions While Gerbil’s performance is comparable to existing state-of-the-art open source k-mer counting tools for small k < 32, it vastly outperforms its competitors for large k, thereby enabling new applications which require large values of k.