I have a fasta file with sample OTUs and would like to annotate this fasta file to produce a new fasta file. It is like the function in Qiime1:
assign_taxonomy.py -i pacbio_otu.fasta -m rdp
I have Qiime 2 on Virtualbox and cannot find a way to do the same for this particular fasta file. Do you have any advice for my situation?
Hello @YinXun, this part of the Moving Picture tutorial discusses how to use
classify-sklearn in QIIME 2. It behaves very similarly to
assign_taxonomy.py in QIIME. It doesn’t output a new fasta file though. It, like
assign_taxonomy.py, outputs a metadata file. Do you need the annotations added specifically to the fasta file for any reason?
Thanks for your response. I am looking to have taxonomy annotation on my pacbio_otu.fasta file as I would like to build my own taxonomy database.
Eventually, I will have this taxonomy database in fasta format, so I could run sintax with other datasets against it. I have downloaded the RDP training set from sintax (https://drive5.com/usearch/manual/sintax_downloads.html) for my case.
Do you have any advice with what I can do for this? Many thanks!
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