Split k-mer analysis (version 2) 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. But 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. Citation

Romain Derelle, Johanna von Wachsmann, Tommi Mäklin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024). Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis. Genome Research, 34(10), 1661–1673.

• Version: 0.4.0
• Added: May, 2025
• Link: https://github.com/bacpop/ska.rust

See which versions are available:

$ module avail ska2

Load one version into your environment and run it:

$ module load ska2/0.4.0
$ ska

Notes from the sysadmin during installation:

$ cd /var/scratch
$ wget https://github.com/bacpop/ska.rust/releases/download/v0.4.0/ska-v0.4.0-ubuntu-latest-stable.tar.gz
$ tar xf ska-v0.4.0-ubuntu-latest-stable.tar.gz
$ sudo mkdir -p /export/apps/ska2/0.4.0
$ sudo cp ska /export/apps/ska2/0.4.0