Which SILVA138 file should be used for --i-reference read and --i-reference taxonomy?


I would like to use SILVA 138 database for taxonomy classification. However, I am not sure which is the correct file to use.
For example the code for taxonomy classification:

qiime feature-classifier classify-consensus-blast
--i-query representative_sequences.qza
--i-reference-taxonomy taxonomy-reference.qza
--i-reference-reads silva-138-reference.qza
--o-classification taxonomy_16S_SILVA138-99
--p-perc-identity 0.99
--p-maxaccepts 1

Where I can download the reference taxonomy.qza and silva-138.qza ?

Much appreciate for the help!

If you are using blast, etc.. you can simply use one of these pre-made sequence files from the Data resources page. These are the files used to make the naïve bayes classifiers.

Also, in order to take full advantage of a "consensus taxonomy" I'd strongly recommend against using --p-maxaccepts 1 otherwise you'll simply be accepting the first, and not necessarily the best, hit to a reference sequence.


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