AGP export

The AGP annotations describe the components that an assembly consists of. This format can be validated by the NCBI AGP validator.

If the exporter is executed on an assembly where the contigs have been updated using a read mapping, the N's in some scaffolds might be resolved or removed. If the exporter encounters such a region, it will give a warning but not stop. If the exporter is executed on an assembly from a previous version of the GWB, it will often stop with an error saying that it encountered more than 10 N's which wasn't marked as a scaffold region. In this case the user would have to rerun the assembly with the current version of the de novo assembler if they wish to be able to export to AGP.

Currently we output two types of annotations in AGP format: