DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k ≤ 32. In contrast, DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.


G. Rizk, D. Lavenier, R. Chikhi. (2013) DSK: k-mer counting with very low memory usage, Bioinformatics, 29(5):652-3 [PDF]

Ready-to-use executable

DSK is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:

maclogo MacOS-X 10.8 or above.
(Intel 64bit processors)
linuxlogo Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)

For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.

Source Code

cpp-logo DSK tool is fully written in C++. Download


DSK binaries and source code are covered by the Affero GPL version 3 license.

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