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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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Feature Request: use pre-computed alignment #130

Open chrisgulvik opened 11 months ago

chrisgulvik commented 11 months ago

Sometimes I have just 1 new isolate I'd like to compare against a larger parsnp run of a couple thousand genomes. Re-running from scratch can take 2+ days to analyze.

Would you consider a non-default option to enable a user to specify just a new dir of assemblies (or even just 1 new one multi-record FastA) and perhaps pull out a pre-computed alignment from the GGR file or something to make this a trivial <1 h run?

bkille commented 11 months ago

Hi @chrisgulvik!

Thanks for opening an issue regarding this feature request. We have plans to support this functionality at some point in the future, but as of right now there is no target date 😞

This has been something we have wanted to enable for some time now, but unfortunately it requires rewriting much of the Parsnp source code.

-Bryce