Can this library be used to accelerate Smith Waterman algorithm powered software, like bwa?

Intel-HLS / GKL

Accelerated kernel library for genomics

MIT License

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Can this library be used to accelerate Smith Waterman algorithm powered software, like bwa? #93

Closed sfchen closed 4 years ago

sfchen commented 6 years ago

If yes, is there any introduction, or any benchmark?

TekTimmy commented 4 years ago

Hi, I'm also missing some documentation how to make the system use these libraries... Do I need to set LD_LIBRARY_PATH? Do I have to move those files somewhere?

rpomaris commented 4 years ago

@sfchen - the short answer is yes. The AVX-512 Smith Waterman Kernel can be used by any tool that uses Smith Waterman. The longer answer is we haven't done this engineering work.
@TekTimmy - I spun your Q out into a separate issue. Our team will address it over there (https://github.com/Intel-HLS/GKL/issues/111)