A new version of the Prokaryotic Genome Annotation Pipeline (PGAP) with several important features is now available on Github.
- In response to several requests we have added the option of running PGAP with Singularity, Podman or any other Docker-compatible executable you wish to use.
- We have also lifted the requirement for internet access in case you have privacy concerns. To run the pipeline without internet access, set the flag
--no-internet. - Are you unsure about the identity of organism you sequenced? We’ve added the Taxonomy-Check module to help you. This module will confirm the organism name or suggest a new taxonomic assignment through average nucleotide identity comparison with type material assemblies from GenBank. The check is currently an optional validation step prior to PGAP.
Try these new features and let us know what you think! Or submit your PGAP-annotated assembly to GenBank. And remember that if you are still improving the assembly and your genome doesn’t pass the pre-annotation validation, you can use the --ignore-all-errors flag to get a preliminary annotation.