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rrwick / Verticall

Recombination-free trees
GNU General Public License v3.0
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repair genomes before creating alignment #5

Closed mcolpus closed 1 year ago

mcolpus commented 1 year ago

Hi Ryan,

I have an alignment I've made with snippy. But some of my genomes contain ambiguous bases so Verticall requires them to be repaired. Should I rerun snippy to make a new alignment first?

Thanks!

rrwick commented 1 year ago

Your assemblies will need to be repaired for Verticall, but you should be able to leave your Snippy alignment as it is. In fact, your assemblies shouldn't be relevant for your Snippy - that should just based on your reads and your reference genome.

The one caveat to this is that your reference genome must be complete and free of ambiguous bases. If that's not the case, then yes, you'll need to fix (or replace) it and then re-run Snippy.

Ryan