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Motivation Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the development of faster pairwise alignment algorithms that can scale with increasing read lengths and production yields. Results In this paper, we present the wavefront alignment algorithm (WFA), an exact gap-affine algorithm that takes advantage of homologous regions between thedoi:10.1093/bioinformatics/btaa777 pmid:32915952 fatcat:yiysfne44nfrbiz6di27nrm6ui