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arXiv · 2004.03033

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

Aleksander Cisłak·Szymon Grabowski
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Abstract

Motivation: 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. Results: 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: github.com/MrAlexSee/sopang

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Aleksander Cisłak, Szymon Grabowski. 2020-04-06. SOPanG 2: online searching over a pan-genome without false positives. https://arxiv.org/abs/2004.03033

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