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mbbu / 16S-mini-project

This is a workflow for 16S rRNA analysis.
https://mbbu.github.io/16S-mini-project/
MIT License
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Taxonomic Classification #7

Closed BryanAbuchery closed 3 years ago

BryanAbuchery commented 3 years ago

Train a classifier (using the qiime feature-classifier fit-classifier-naive-bayes model)

  1. Obtain the SILVA 132 or Greengenes 13_8 (latest releases for both) databases for 16S analysis.
  2. Extract representative sequences and taxonomy files.
  3. Train a classifier using the Naive Bayes model using database of choice.
  4. Use the classifier to assign taxonomies for dataset.
  5. Construct taxonomy barplots to explore microbiome profiles (our dataset in this case).
BryanAbuchery commented 3 years ago

Taxonomic classification was done after training a Greengenes classifier on the Naive Bayes model as is demonstrated in Qiime2 E2E Analysis/scripts/train_classifier_gg.sh