GitHub / Mangul-Lab-USC / review-technology-dictates-algorithms

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.

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Topics: genome-analysis, heuristics, hifi-read, hts, illumina-sequencing, nanopore-sequencing, needleman-wunsch, pacbio-sequencing, read-alignments, read-mapping, sequence-alignment, smith-waterman

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