SVPS, pairwise whole genome alignment-based structural variant identification^*

This paper proposes a whole genome alignment-based structural variant (SV) identification method that uses chromosome-level genome assemblies. The method detects the presence of SVs between two genomes by scanning whole genome alignments for patterns corresponding to different SV types. The process is implemented as a software pipeline named Structural Variant Pattern Evidence Scan, or SVPS, made with the Snakemake [1] workflow management system. For validation, SVPS was assessed through two case studies on two plant genomes – Brassica nigra and Arabidopsis thaliana. Alignment sensitivity significantly impacted SVPS’s results, causing differences in the number, locations, and sizes of SVs reported. SVPS detected significantly more SVs than other whole genome alignment SV tools. Still, the high accuracy of its results when evaluated with another independent aligner demonstrates that there is value in its higher sensitivity. SVPS is available publicly under MIT license at https://github.com/USask-BINFO/SVPS.