Hi @Nicholas_Bokulich. Finally getting around to testing this.
I've imported a multi-fasta of reference samples sequenced with Sanger sequence using qiime tools import --type 'FeatureData[Sequence'.
Here's a screenshot of the first few sequences in the FASTA:
Based on these instructions, I created a headerless taxonomy file with just the accession number from my FASTA. As with NCBI, I assumed Qiime would consider everything left of the first space in the header to be the accession number.
Both the taxonomy and sequences import without a problem, but if I just merge them to my GenBank taxonomy and sequences, I don't really have a way of knowing whether the new taxonomy and sequences that I imported are properly connected.
Is there a way to verify that? Or can you affirm that this should work?
Alternatively, it seems you can use the feature IDs of the sequences, or the accession number in the taxonomy file. Is there an easy way to find the feature IDs from a FASTA that I just imported?
Thanks as always for your help!