MSA to GFA

[dbrami]

Hello, Thank you for this wonderful, cross-platform tool! Is there a way to use this tool to go from an existing MSA to GFA? This would be my "starter" graph; Then I would use your upcoming "incremental" option to add either new MSA's or new sequences to it...

[yangao07]

Are you referring to the MSA format output of abPOA or other styles of MSA?

[dbrami]

Hi, I’m thinking of a fasta style MSA

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Are you referring to the MSA format output of abPOA or other styles of MSA?

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[yangao07]

Can you describe in more details, or give an example?

[dbrami]

Of course, Here's an example of Coronavirus alignment from GISAID first_20_msa_0201.fasta.gz

[dbrami]

Something that does the same thing as https://github.com/hanzou666/msa2gfa But the above is a pure python implementation with a bunch of for loops - very slow.

[subwaystation]

If you just want to go from MSA to GFA, then you could try out vg construct.

construct from a multiple sequence alignment:
    -M, --msa FILE         input multiple sequence alignment
    -F, --msa-format       format of the MSA file (options: fasta, clustal; default fasta)
    -d, --drop-msa-paths   don't add paths for the MSA sequences into the graph

[yangao07]

@dbrami I do not plan to add a feature of converting MSA to GFA in abPOA. Right now, the latest abPOA (v1.1.0) can incrementally align sequences to an existing GFA or MSA. For your case, maybe you can align your sequence to the MSA using abPOA directly.

Yan

[dbrami]

Dear @subwaystation and @yangao07, All though your answers are seemingly brief and seemingly simple, these have been a tremendous help. Thank you