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ska2 website  

Split k-mer analysis (SKA version 2 or SKA2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses. SKA can only align SNPs further than the k-mer length apart, and does not use a gap penalty approach or give alignment scores. However, the advantages are speed and flexibility, particularly the ability to run on a reference-free manner (i.e. including accessory genome variation) on both assemblies and reads.

Note: This is a reimplementation of Simon Harris' SKA package ( in the rust language by Johanna von Wachsmann, Simon Harris, and John Lees.

Environment Modules

Run module spider ska2 to find out what environment modules are available for this application.

System Variables

  • HPC_SKA2_BIN - installation directory
  • HPC_SKA2_DIR - installation directory

Additional Information

Additional details and usage are documented here:


If you publish research that uses ska2 you have to cite it as follows:

Harris SR. 2018. SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology. bioRxiv 453142 doi: