A scan-based reformulation of the striped Smith-Waterman lazy-F loop achieves O(n/p + log(p)) per iteration and improves BWA alignment speed on AVX2 and AVX512VL.
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De(con)struction of the lazy-F loop: improving performance of Smith Waterman alignment
A scan-based reformulation of the striped Smith-Waterman lazy-F loop achieves O(n/p + log(p)) per iteration and improves BWA alignment speed on AVX2 and AVX512VL.