search

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
175 stars 51 forks source link

Coordinates in the output file "Recombination predictions in GFF format" #330

Closed valery-shap closed 2 years ago

valery-shap commented 2 years ago

Hello, Thank you for the great tool. Sorry if my question is obvious but I couldn't find the answer in manual or issues. Are the coordinates of .recombination_predictions.gff file correspond to the alignment file that was used for input? not the coordinates of the reference genome. Valery

nickjcroucher commented 2 years ago

Apologies this wasn't clearer - the positions are relative to the alignment, not the reference sequence. Gubbins treats all sequences equally (i.e. it is not aware of a reference).

nickjcroucher commented 2 years ago

Clarified in manual in a2abf61.