AGP export (legacy)
The AGP exporter has been made legacy and will be retired in a future release of the CLC Genomics Workbench. From March, 2025 GenBank stopped accepting AGP files for genome submissions.
AGP annotations in a de novo assembly 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 38.1).
Figure 38.1: 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:
- Contig a non-redundant sequence not containing any scaffolded regions.
- Scaffold the estimated gap region between two contigs.