I was wondering if there's a streamlined way of getting the "representative" genome for a particular species. What I'm looking for is an automated way of retrieving a genome assembly and annotation for all bacterial species in, e.g. Kraken2 output. The most popular databases for Kraken2 are made from RefSeq, so I'd imagine there should be a relatively easy way to match Taxonomy ID/species name to a RefSeq ID.
Any advice would be appreciated, as always!
All the best