SOPanG 2: online searching over a pan-genome without false positives
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
Keywords
Cite
@article{arxiv.2004.03033,
title = {SOPanG 2: online searching over a pan-genome without false positives},
author = {Aleksander Cisłak and Szymon Grabowski},
journal= {arXiv preprint arXiv:2004.03033},
year = {2020}
}