Jul 20, 2023

C++ implementation of the partial order alignment (POA) algorithm

Spoa SIMD POA is a c++ implementation of the partial order alignment POA algorithm as described in 10.1093/bioinformatics/18.3.452 which is used to generate consensus sequences. It supports three alignment modes local Smith-Waterman, global Needleman-Wunsch and semi-global alignment overlap, and three gap modes linear, affine and convex piecewise affine. It also supports Intel SSE4.1+ and AVX2 vectorization marginally faster due to high latency shifts, SIMDe and dispatching.

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