We have updated the collection of representative and reference assemblies for Bacteria and Archaea to better reflect the taxonomic breadth of the prokaryotes in RefSeq. We chose the 11,478 representative assemblies in the new collection from the 180,000+ prokaryotic assemblies in RefSeq today. We have selected one representative or reference assembly for every species based on several criteria including contiguity, completeness and whether the assembly is from type material. We have also updated the reference and representative microbial Blast database to reflect these changes. This reference and representative set will be updated three times a year to reflect changes in RefSeq. In addition, as we announced on Feb 14, we have reduced the number of reference genome assemblies — the subset of representative assemblies with annotation provided by outside experts — to 15. See the list in our previous post . We have re-annotated the 104 assemblies that are no longer reference with or Prokaryotic Genome Annotations Pipel (PGAP).
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