We are making changes to the set of bacterial and archaeal RefSeq Reference and Representative assemblies in February 2020.
- We will reduce the number of Reference assemblies to 15 that have annotation provided by outside experts (Table 1) and re-annotate the 105 other current Reference assemblies using the latest Prokaryotic Genome Annotation Pipeline (PGAP) software. The re-annotated assemblies will lose reference status.
- We will reassess and revise the set of Representative assemblies so that there is one assembly per species to better reflect the taxonomic diversity of the RefSeq bacterial and archaeal assemblies.
Table 1. The set of 15 prokaryotic assemblies that will retain Reference status. These are regularly updated by an involved community of microbiologists.
These improvements have an impact on the following resources:
- Microbial genomes BLAST
- Updated Reference and Representative genomes databases.
- Fewer reference assemblies.
- Different set of representative assemblies.
- Updated list of Reference genomes.
- Changes to the assemblies listed in the “Representative” section of the individual Genome organism pages.
- Reduced list of Reference assemblies (began with software version 4.11, released in January 2020).
- Protein alignments annotated on the Reference assemblies at the genus level given higher weight. This is a change compared to prior PGAP software where alignments of proteins on the reference genome(s) in the same clade were given higher weight.