René Rahn1, David Weese1, Knut Reinert1. 1. Department of Mathematics and Computer Science, Freie Universität Berlin, Takustr. 9, 14195 Berlin, Germany.
Abstract
MOTIVATION: Next-generation sequencing (NGS) has revolutionized biomedical research in the past decade and led to a continuous stream of developments in bioinformatics, addressing the need for fast and space-efficient solutions for analyzing NGS data. Often researchers need to analyze a set of genomic sequences that stem from closely related species or are indeed individuals of the same species. Hence, the analyzed sequences are similar. For analyses where local changes in the examined sequence induce only local changes in the results, it is obviously desirable to examine identical or similar regions not repeatedly. RESULTS: In this work, we provide a datatype that exploits data parallelism inherent in a set of similar sequences by analyzing shared regions only once. In real-world experiments, we show that algorithms that otherwise would scan each reference sequentially can be speeded up by a factor of 115.
MOTIVATION: Next-generation sequencing (NGS) has revolutionized biomedical research in the past decade and led to a continuous stream of developments in bioinformatics, addressing the need for fast and space-efficient solutions for analyzing NGS data. Often researchers need to analyze a set of genomic sequences that stem from closely related species or are indeed individuals of the same species. Hence, the analyzed sequences are similar. For analyses where local changes in the examined sequence induce only local changes in the results, it is obviously desirable to examine identical or similar regions not repeatedly. RESULTS: In this work, we provide a datatype that exploits data parallelism inherent in a set of similar sequences by analyzing shared regions only once. In real-world experiments, we show that algorithms that otherwise would scan each reference sequentially can be speeded up by a factor of 115.
Authors: Jordan M Eizenga; Adam M Novak; Jonas A Sibbesen; Simon Heumos; Ali Ghaffaari; Glenn Hickey; Xian Chang; Josiah D Seaman; Robin Rounthwaite; Jana Ebler; Mikko Rautiainen; Shilpa Garg; Benedict Paten; Tobias Marschall; Jouni Sirén; Erik Garrison Journal: Annu Rev Genomics Hum Genet Date: 2020-05-26 Impact factor: 8.929