  A basic task in bioinformatics is the counting of $k$-mers in genome strings.
The $k$-mer counting problem is to build a histogram of all substrings of
length $k$ in a given genome sequence. We present the open source $k$-mer
counting software Gerbil that has been designed for the efficient counting of
$k$-mers for $k\geq32$. Given the technology trend towards long reads of
next-generation sequencers, support for large $k$ becomes increasingly
important. While existing $k$-mer counting tools suffer from excessive memory
resource consumption or degrading performance for large $k$, Gerbil is able to
efficiently support large $k$ without much loss of performance. Our software
implements a two-disk approach. In the first step, DNA reads are loaded from
disk and distributed to temporary files that are stored at a working disk. In a
second step, the temporary files are read again, split into $k$-mers and
counted via a hash table approach. In addition, Gerbil can optionally use GPUs
to accelerate the counting step. For large $k$, we outperform state-of-the-art
open source $k$-mer counting tools for large genome data sets.
