- Course overview
- Search within this course
- Environmental DNA
- DNA metabarcoding and its applications
- Workflow for eDNA metabarcoding
- DADA2 for analysing metabarcoding data
- Statistics principles in data analysis
- Advances in biodiversity exploration
- Open data resources for eDNA
- Bringing data to life: Data management and sharing
- Further learning
- Your feedback
- References
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Open resources for assigning taxonomy
Most pipelines or methods for processing metabarcoding data include a taxonomic classifier within their workflow, with some offering multiple options to choose from. The choice of classifier depends on the taxonomic composition of your samples or target, as well as the suitability of the reference database. Many research communities have a favoured approach, however, the RDP classifier is the most widely used approach in various pipelines. Some of the widely used open resources and their associated taxonomic classifier are listed below:
- DADA2: Uses the RDP Naive Bayesian Classifier algorithm as the taxonomic classifier (many reference databases for biodiversity studies provide formatted versions of data which is compatible with DADA2 platform).
- QIIME2: Includes many options for taxonomic classifiers such as BLAST, BLAST+, RDP Naive Bayesian Classifier algorithm, SortMeRNA, SINTAX, UCLUST, etc.
- USEARCH: Uses the RDP Naive Bayesian Classifier algorithm and SINTAX as taxonomic classifiers.
- Mothur: Uses the RDP Naive Bayesian Classifier algorithm as the taxonomic classifier
As mentioned earlier, you will need a suitable reference database for taxonomy analysis. On the next page, you will find various database options to choose from for your research.
