I am having trouble with the core gene alignment generated by Roary.
I used Prokka to annotate 69 genomes of bacteria belonging the same genus. Then, I used the gff3 files in Roary to generate a core gene alignment.
Everything worked out nicely expect that I am not able to use that core gene alignment because the names given to the genomes are very weird (for example “dataset_00b65bd2-68c1-4486-92a6-8c88170ac99d”).
I am not able to track back those names to find out to which genomes they correspond because they are not the names of the ggf3 files nor the names of the sequence region. I don’t know if I am doing something wrong or if it is a bug.
Has someone experienced something similar?
Thanks for your help.