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Faster Needleman-Wunsch rapid global alignment of two sequences?

Hi all, A student of mine has been using stretcher from EMBOSS. Is there a faster program that ideally works easily with:

program input1.fa.gz input2.fa.gz

where we would have a multifasta as output and some stats?

Thank you in advance!

needleman-wunsch alignment
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written by Gabriel R. Gabriel R.

I would have thought needle from EMBOSS would be the option to use.

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written by GenoMax GenoMax

needle is great! but it does not handle sequences of 100k or so.

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written by Gabriel R. Gabriel R.

Then you may want to see if a program like lastz (LINK) may be useful.

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written by GenoMax GenoMax

2 answers

If you are willing to do some coding I think https://github.com/smarco/WFA2-lib is among the fastest global aligners, the repo has C++ examples too

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written by b.contreras.moreira • b.contreras.moreira

I know about it, isn't there a simple C++ static binary?

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written by Gabriel R. Gabriel R.

Not sure, you might ask in the repo, please share here the response if you find it

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written by b.contreras.moreira • b.contreras.moreira

I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.

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written by Gabriel R. Gabriel R.

I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test out as well: APA & APA2: A* Pairwise Aligner.

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written by DGTool • DGTool

We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR as far as we know.

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written by Gabriel R. Gabriel R.

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