Curate Silva database- add sequences

Commands in mothur
1

Hi,

I am working with an 18S v8-v9 dataset, and am having trouble classifying otus using the SILVA database. The sequences, using the MiSeq SOP defaults and the SILVA taxonomy file do not classify (additionally, using lowest-quality cutoffs, I get unexpected outputs). The sequences from the top 5 OTUs, when searched against the NCBI database, suggest they represent an organism not present in the SILVA taxonomy file.

Is there a way to ‘add’ sequences to the SILVA align and taxonomy files (and if so, what would be required for adding sequences)?


Thank you in advance!
2

If you look at the format of the silva files you should be able to see what you need to add. I would suggest pulling the sequence from the silva website since they’ll have the same alignment and classification structure.

Pat