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philipc / gkl-rs

Rust bindings for Intel Genomics Kernel Library (GKL)
Apache License 2.0
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Discussion: Feasibility of developing a needleman-wunsch global aligner #15

Closed rhysnewell closed 2 years ago

rhysnewell commented 2 years ago

Hi Philip,

Just brainstorming here. I wanted to hear your thoughts on the possibility of taking the existing smith-waterman code and altering it to perform a global alignment instead. The only reason I'd want to do this is to see how GKL-rs would compare against currently existing global pairwise aligners, like WFA https://github.com/smarco/WFA2-lib

I'm hoping to take this on as a side project, but I just want to hear if you think GKL-rs is currently adaptable as it currently exists.

Cheers, Rhys

philipc commented 2 years ago

I think it already is global alignment: https://github.com/broadinstitute/gatk/issues/6576#issuecomment-1003504446

But either way, yes I think it is feasible to adapt GKL-rs to handle both.

rhysnewell commented 2 years ago

Oh easy as, I remember seeing this comment of yours ages ago but must have forgotten about it. Glad to know it's easy, just wanted to double check there wasn't some weirdness happening in the background that would global/local alignments difficult.

Knowing it is already global, i'll go ahead and play around with it. Thanks again!

philipc commented 2 years ago

That might have been from #11. So there might still be some overhang differences to account for in order to get the same results as WFA2-lib, but that won't be hard.

rhysnewell commented 2 years ago

Alright, nice I'll keep you posted then