SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide explains how to create a SNP alignment from a skf file using the different options implemented in the command ska align (here using ska v0.3.5). Recommended command line For those in a hurry, the recommended command line for filtering for precise SNP calling is: ska align --no-gap-only-sites --filter-ambig-as-missing --filter no-ambig-or-const Breakdown using an example In this example, let’s consider a skf file generated using k=51 from Illumina sequencing reads of 45 Mycobacterium tuberculosis isolates collected by the UKHSA, and belonging to the same transmission cluster (i.

SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide will explain how to use SKA to build a phylogenetic tree for different Escherichia coli lineages in a few minutes. Although SKA is tailored more towards analysing variation within a lineage, tree-building ends up working fine for the whole species but requires more memory. Why SKA is good for building phylogenetic trees The basic approach to building a tree with SKA is to generate a SNP alignment using split k-mers and then feed that to a tree building algorithm of choice.