During the whole genome sequence submission process of bacteria in NCBI, there comes a field "whether you want to annotate the genome using NCBI Prokaryotic Genome Annotation Pipeline (PGAP)". We are confused about whether we need to follow the workflow described in NCBI and annotate it from our end or it will do it by itself with the sequence uploaded?
HI Kumari,
It is automated and done by NCBI. I think it is just the description of what they are going to do, not what you have to do.
Frank
Frank R Burns Thank you so much. Do we need to submit the raw sequence reads or the assembled genome?
Hi Kimari,
Generally you create a bio project at NCBI that includes a submission of the individual reads to the short read archive (SRA) and include the bio project ID with the assembled genome submission. This provides a link back to the original reads if anyone wants to try an alternate assembly.
Good luck!
Thank you Frank R Burns Abhijeet Singh
By Short Read Archieve, what is meant, the assembled genome in scaffolds, or the raw infiltered sequence reads that are generated during sequencing.
In our case, the raw sequence reads are 850 times the final genome assembled.
Please help.
Frank R Burns
Thank you sir for clarifying my doubts. Sir, for whole genome submission which submission tool should be used: Genome submission portal or SRA submission portal?