Hi
This may be useful to someone.
I'm new to qiime but while learning it over the past week I made a q2 usable version of the HITdb classifier from this paper: Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database "Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database" . It's a gut specific 16S database and here I used their *.fna (fasta) files and the taxonomy text file from the supplementary zip file. I believe their classifier only worked in qiime1. The q2 friendly version of the Ritari et al. database works well and returns similar results to the 30MB V4 greengenes classifer when viewed using q2 taxa bar-plot. Note I've trimmed for the EMP V4 region amplicon 515F-806R.
Here is my code:
#MAKE CLASSIFIER
qiime tools import
--type 'FeatureData[Sequence]'
--input-path HITdb_sequences.fna
--output-path HITdb_sequences.qza
qiime tools import
--type 'FeatureData[Taxonomy]'
--source-format HeaderlessTSVTaxonomyFormat
--input-path HITdb_taxonomy_qiime.txt
--output-path HITdb_taxonomy_qiime.qza
qiime feature-classifier extract-reads
--i-sequences HITdb_sequences.qza
--p-f-primer GTGCCAGCMGCCGCGGTAA
--p-r-primer GGACTACHVGGGTWTCTAAT
--p-trunc-len 250
--o-reads HITdb_sequences_V4.qza
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads HITdb_sequences_V4.qza
--i-reference-taxonomy HITdb_taxonomy_qiime.qza
--o-classifier HITdb_classifier.qza
#THEN CLASSIFY USING YOUR CLASSIFIER
qiime feature-classifier classify-sklearn
--i-classifier HITdb_classifier.qza
--i-reads rep-seqs.qza
--o-classification HITdb_taxonomy_qiime2.qza
qiime metadata tabulate
--m-input-file HITdb_taxonomy_qiime2.qza
--o-visualization HITdb_taxonomy_qiime2.qzv
qiime taxa barplot
--i-table table.qza
--i-taxonomy HITdb_taxonomy_qiime2.qza
--m-metadata-file sample-metadata.tsv
--o-visualization HITdb_taxa-bar-plots2.qzv
qiime tools view HITdb_taxa-bar-plots2.qzv
HITdb_classifier.qza (2.9 MB)