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Wfa2-lib
Jul 20, 2023
Exact gap-affine algorithm using homology to accelerate alignment
The wavefront alignment WFA algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Unlike traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time Ons+s^2, proportional to the sequence length n and the alignment score s, using Os^2 memory or Os using the ultralow/BiWFA mode. Moreover, the WFA algorithm exhibits simple computational patterns that the modern compilers can automatically vectorize for different architectures without adapting the code.
Checkout these related ports:
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