RDP COI Classifier

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Hi @Newt,

There are quite a few tutorials in this forum on how to make your own COI classifier.

Otherwise, if you want a quick way to import the pre-curated RDP formatted files that you linked to, all you need to do is run the following commands:

  1. Extract FASTA header (taxonomy) from RDP FASTA file:
    This command will only process the FASTA header lines. It will remove the > character and then replace the first space character with a tab '\t' character, then write the ID and taxonomy to file. There are many other ways to do this, I just quickly did this as an example. :slight_smile: 
grep '^>' mytrainseq.fasta | sed 's/>//' | sed 's/ /\t/' > taxonomy.tsv
  1. Import taxonomy into QIIME 2:
 qiime tools import \
  --input-path taxonomy.tsv \
  --type 'FeatureData[Taxonomy]' \
  --input-format 'HeaderlessTSVTaxonomyFormat' \
  --output-path taxonomy.qza
  1. Import RDP FASTA file:
    We'll use 'MixedCaseDNAFASTAFormat' as these files have non-standard IUPAC lower case nucleotides. 
qiime tools import \
    --input-path mytrainseq.fasta \
    --type 'FeatureData[Sequence]' \
    --input-format 'MixedCaseDNAFASTAFormat' \
    --output-path mytrainseq.qza
  1. Optionally perform further curation with RESCRIPt.
    For example, dereplicate the sequence data (reduce data size), extract an amplicon region, etc... Something like this: 
qiime rescript dereplicate \
    --p-rank-handles 'disable' \
    --p-threads 8 \
    --i-sequences mytrainseq.qza \
    --i-taxa taxonomy.qza \
    --o-dereplicated-sequences derep-seqs.qza \
    --o-dereplicated-taxa derep-taxa.qza
  1. Train and use the classifier:
    Optionally use other methods like classify-consensus-blast or classify-consensus-vsearch. Or replace the inputs with the optional dereplication outputs from the previous command. 
qiime feature-classifier fit-classifier-naive-bayes \
  --i-reference-reads mytrainseq.qza \
  --i-reference-taxonomy taxonomy.qza \
  --o-classifier classifier.qza

qiime feature-classifier classify-sklearn \
  --i-classifier classifier.qza \
  --i-reads rep-seqs.qza \
  --o-classification assigned-taxonomy.qza
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