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lenaschimmel / sc2rf

SARS-Cov-2 Recombinant Finder for fasta sequences

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ENH: Accept MAPLE file as alternative to fasta

corneliusroemer opened this issue · comments

commented

I think it could speed up the algorithm quite a bit if you accepted sequences in MAPLE format rather than fasta.

Maple contains basically all the info you want, all the mutations. So there's be no need to recompute.

I can see if we can produce MAPLE files from Nextclade. It would make sense to produce a human readable complete output.

It's probably a bit early to implement this before there are good tools to produce maple files - but I think it's neat that this format would speed up sc2rf a lot!

https://www.biorxiv.org/content/10.1101/2022.03.22.485312v1.full