We have released a new version of the Prokaryotic Genome Annotation Pipeline (PGAP), available on GitHub. The new release includes the ability to ignore pre-annotation validation errors (–ignore-all-errors). This new feature allows you to produce a preliminary annotation for a draft version of the genome, even one that contains vector and adapter sequences or that is outside of the size range for the species. This draft annotation should be helpful with your ongoing work on the genome assembly. Please keep in mind that these pre-annotations and assemblies with contaminants or other errors are not suitable for submission to GenBank.
Another new feature allows you to provide the name of the consortium that generated the assembly and annotation so that this information appears in the final GenBank records. For more details, consult our guidelines on input files.
See our previous post and our documentation for details on how to obtain and run PGAP yourself.
Next on our to-do list is a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned!