PEMA investigating metabarcoding

12S analysis

Set marker_gene: 12S in the parameters file; 12S is mostly used for fish and other vertebrates.

For the clustering, set clustering_algo to swarm (ASVs) or vsearch (OTUs); see 16/18S analysis.

Taxonomy assignment

  • RDPClassifier (classifier: rdp) with the PEMA-trained 12S database: set database: 12S_v200 and databases_dir to a folder of yours in the rdp section; PEMA downloads the database from Zenodo the first time it is used. 12S amplicons are short, so a confidence lower than the default 0.8, such as 0.5, usually gives more assignments to genus and species.
  • crest4 (classifier: crest) with database: mitofish, the crest4 database built from MitoFish.

You can also use your own reference database; see Training the RDPClassifier and Training the CREST classifier.