I want to perform a genome comparison on a group of isolates. I want to look into two broad groups of taxa and compare the accessory genome in each group. I have been using prokka (v1.12) and roary (v3.8.2) to do this but it appears the accessory_binary_genes.fa file is actually an untrue representation.Note: gene_presence_absence.Rtab does contain all the full presence/ absence for accessory gene sets. Despite this Im still unhappy with the nomenclature of the gene groups [issue for another day] [github issue 335] Your best to ignore the accessory_binary_genes.fa file. It is just for creating a quick and dirty tree with FastTree. The file itself is filtered to remove very common and not common variation to speedup the tree generation, hence the difference in numbers.The top 5% and bottom 5% are excluded. It is truncated at 4000 genes.I've been looking into alternative pipelines and a new software BPGA looks promising. Does anyone have experience with this?I essentially want a tool which will give me the core and accessory gene sets, without the noise from partial gene hits.
What tools can I use for a bacterial core/pan genome pipeline?
genome;software recommendation