Strobealign: flexible seed size enables ultra-fast and accurate read alignment

Abstract

Read alignment is often the computational bottleneck in analyses. Recently, several advances have been made on seeding methods for fast sequence comparison. We combine two such methods, syncmers and strobemers, in a novel seeding approach for constructing dynamic-sized fuzzy seeds and implement the method in a short-read aligner, strobealign. The seeding is fast to construct and effectively reduces repetitiveness in the seeding step, as shown using a novel metric E-hits. strobealign is several times faster than traditional aligners at similar and sometimes higher accuracy while being both faster and more accurate than more recently proposed aligners for short reads of lengths 150nt and longer. Availability: https://github.com/ksahlin/strobealign