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 if you select the option "Update contigs" (figure 5.13).
Figure 5.12: Select "update contigs" by ticking the box if you want to resolve scaffolds based on a read mapping.
If the exporter encounters such a region, it will give a warning but not stop. If the exporter is executed on an assembly from GWB versions older than 6.5, 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 GWB version 6.5 or newer 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:
- Contig a non-redundant sequence not containing any scaffolded regions.
- Scaffold the estimated gap region between two contigs.