rrwick / Verticall

Recombination-free trees
GNU General Public License v3.0
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Any other way to make pseudo-alignment from fasta assemblies? #3

Closed samlipworth closed 1 year ago

samlipworth commented 1 year ago

Hi Ryan,

I'm trying to make a tree from 9000ish asssemblies so this obviously seems like a perfect solution - the problem I'm encountering is that the generate_ska_alignment.py script crashes with the error message: /bin/sh: Argument list too long - appreciate this is not your script, but any ideas for other methods to generate this?

Thanks, Sam

samlipworth commented 1 year ago

Tried subsetting them - doesn't even work with a few thousand unfortunately.. I think the solution here might be to run the assemblies through snippy.

samlipworth commented 1 year ago

closing this because snippy seems a nice solution