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 if you select the option "Update contigs" (figure 35.13).

Image denovo_update_contigs
Figure 35.13: 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.

Currently we output two types of annotations in AGP format: