This is a basic question but I couldn’t find this topic in the forum so here goes -
When you are ready to submit a paper that includes amplicon sequencing data - how do you submit the sequences/data to NCBI to get accession numbers? Back in the day you would do individual/batch submission, but then the assumption was that each sequence was obtained independently. Can you still use batch submission for amplicon data? If so, what do you put under ‘isolate’ (its supposed to be a unique alphanumeric code describing the sample from which each sequence was obtained). Alternatively - are you supposed to submit the whole project, including the raw data? Wouldn’t this, in fact, lead to a less informative/accessible submission, or are the amplicons then somehow incorporated into Genebank?
In our case we are really tempted to submit individually since we used targeted amplicon sequencing, so we only have 25 sequences, all from the same genus.
I would be happy to hear from people who have experience dealing with NCBI submission of amplicon data - many thanks!