Introduction

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.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.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.

Publications

  1. Gerbil: a fast and memory-efficient k-mer counter with GPU-support.
    Cite this
    Erbert M, Rechner S, Müller-Hannemann M, 2017-01-01 - Algorithms for molecular biology : AMB

Credits

  1. Marius Erbert
    Developer

    Institute of Computer Science, Martin Luther University Halle-Wittenberg, Germany

  2. Steffen Rechner
    Developer

    Institute of Computer Science, Martin Luther University Halle-Wittenberg, Germany

  3. Matthias Müller-Hannemann
    Investigator

    Institute of Computer Science, Martin Luther University Halle-Wittenberg, Germany

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Summary
AccessionBT005765
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionGermany
Submitted ByMatthias Müller-Hannemann