Faster Needleman-Wunsch rapid global alignment of two sequences?

Question

[Gabriel R.]

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!

[GenoMax]

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

[Gabriel R.]

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

[GenoMax]

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

Answer 1

[b.contreras.moreira]

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

[Gabriel R.]

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

[b.contreras.moreira]

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

[Gabriel R.]

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

Answer 2

[DGTool]

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.

[Gabriel R.]

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.