I have annotated a genome successfully with PROKKA. I can upload the genome to NCBI, but I cannot upload the annotation. PROKKA does not produce files in the correct format, and I cannot find any examples of what the correct format should look like, nor do any of the online compatability checkers clearly state what the problem is. So, other than as a supplementary file on the publication, where do I upload the PROKKA annotation files (available in .fasta, .asn1, .genbank, .gff, .gbff, .json, and .sqn formats)?
Hi Matan Shelomi When annotating with prokka you have to use the --compliant flag . This will generate NCBI compliant files.
Matan Shelomi If your genomes are bacterial isolates you can also do a visual comparison using BRIG software. I made a tutorial about that here : https://youtu.be/pobQgE4z-5Q
Submit via pgap pipeline on NCBI. You just need your bacterial genome in fast format. It will automatically find the errors if any, annotate and submit your genome.
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