Taxonomic Data: Using 18S-Nemabase in Qiime2 instead of Silva?

You could simply download the premade SILVA sequence and taxonomy files from the Data resources page, and filter the sequences using qiime taxa filter-seqs ... like so:

If we just want to provide only eukaryotic outgroup taxa, but no SILVA nematode sequences you would run the command below. So, we are removing all Bacterial and Archaeal sequences. We'll also remove the Nematoda, as we do not want to pollute our new NemaBase database. You can also simply just remove the Nematoda, and leave the Archaea and Bacteria there as decoys / outgroups. You may have to play around and see which works best.

qiime taxa filter-seqs \
    --i-sequences silva_sequences.qza \
    --i-taxonomy silva_taxonomy.qza \
    --p-exclude Nematoda,Bacteria,Archaea \
    --o-filtered-sequences  silva_euk_outgroup_seqs.qza

Now that we have our filtered SILVA database, we'll want to remove the taxonomy information for those sequences we removed. So, we can run:

qiime rescript filter-taxa \
    --i-taxonomy silva_taxonomy.qza \
    --m-ids-to-keep-file  silva_euk_outgroup_seqs.qza
    --o-filtered-taxonomy  silva_euk_outgroup_taxonomy.qza

Now we have two files we can merge to our NemaBase files: silva_euk_outgroup_seqs.qza and silva_euk_outgroup_taxonomy.qza. Assuming you've been able to import the NemaBase files.

Now we can merge:

qiime feature-table merge-seqs \
    --i-data  silva_euk_outgroup_seqs.qza  nemabase_seqs.qza \
    --o-merged-data nemabase_w_silva_euk_outgroup_seqs.qza

qiime feature-table merge-taxa \
    --i-data silva_euk_outgroup_taxonomy.qza nemabase_taxonomy.qza \
    --o-merged-data nemabase_w_silva_euk_outgroup_taxonomy.qza

Assuming there are similar taxonomic rankings (d__,p__,c__,o__,f__,g__,s__) you should now be able to train your classifier. If needed you can play around with qiime rescript edit-taxonomy ... to fix things.

qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads nemabase_w_silva_euk_outgroup_seqs.qza \
  --i-reference-taxonomy nemabase_w_silva_euk_outgroup_taxonomy.qza \
  --o-classifier nemabase_w_silva_euk_outgroup_classifier.qza

This should help you get started. :slight_smile:

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