SOPanG 2: online searching over a pan-genome without false positives

The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any) match the entire query. We augment the ED string with sources (individuals' indexes) and propose an extension of the SOPanG (Shift-Or for Pan-Genome) tool to report only true positive matches, omitting those not occurring in any of the haplotypes. The additional stage for checking the matches yields a penalty of less than 3.5% relative speed in practice, which means that SOPanG 2 is able to report pattern matches in a pan-genome, mapping them onto individuals, at the single-thread throughput of above 430 MB/s on real data. Availability and implementation: SOPanG 2 can be downloaded here: this http URL. Contact: sgrabow@kis.this http URL