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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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identifying the donor of recombination events #377

Closed evolbeginner closed 1 year ago

evolbeginner commented 1 year ago

I have a question regarding the identification of the direction of recombination events. While I realize that gubbins may not tell the direction of a recombination event (indicated in the _recombinationpredictions.gff file), I was wondering if it is possible to tell the donor by the following strategy. Use the reconstructed sequence at the node of interest (denoted as _nodea) to search against the sequences of all other nodes, tips included. If it maps well to the sequence of another ancestral node (denoted as _nodei), then does it provide evidence that the recombination is from _nodei to _nodea? The strategy may sound naïve but I was just wondering if it makes sense. Thanks!

nickjcroucher commented 1 year ago

Gubbins effectively asssumes that the donor of the recombination is outside the tree, i.e. your analysed dataset should only consist of closely-related isolates (e.g. a strain defined by PopPUNK). So looking for the donor within the tree is not expected to be effective. This is an example of a post-Gubbins analysis where we have searched for the donor of recombinations in a post hoc analysis, using a diverse database of possible donors - that is what I would recommend.