Can Gubbins be used on eukaryotic genomes?

nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

http://nickjcroucher.github.io/gubbins/

GNU General Public License v2.0

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Can Gubbins be used on eukaryotic genomes? #401

Closed Adamtaranto closed 7 months ago

Adamtaranto commented 7 months ago

Can Gubbins be used on sexually recombining haploid fungal genomes? The reference genome will have multiple chromosomes.

nickjcroucher commented 7 months ago

Yep - it's imperfect, because recombinations can be falsely inferred to go over the edge of chromosome boundary, but we have applied it previously to such genomes and it can do a good job (depending on the sampling of the collection and biology of the species).