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Tongdongq / darwin-gpu

GPU accelerated version of Darwin, a DNA alignment algorithm
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Pairwise alignment with GACT #3

Open quim0 opened 1 year ago

quim0 commented 1 year ago

Hello,

I'm interested in using GACT to perform sequence-to-sequence pairwise alignment. Can the GACT implementation be used as a standalone tool or library?

Thank you

Tongdongq commented 1 year ago

It's been a while but I think GACT can be used. You can refer to the original paper to find more explanation on the workings.

quim0 commented 1 year ago

I understand that the GACT algorithm has the capability of pairwise alignment, however, my interest is to test the GPU implementation of GACT.

I'm interested in having a binary to do pairwise alignment of two .fasta files or having some kind of API into which I can feed sequences to just do pairwise alignment. Is that possible?

Thanks

Tongdongq commented 1 year ago

I see, I think that'll be difficult. You could try removing the z_compile.sh check in darwin.cpp, lines 34-36 and using make. This would create a binary which includes the D-SOFT filtering. Extracting the GACT_Batch call is probably more difficult, and requires preprocessing like compressing the bases into 2-bit values.