This repository contains an R based workflow based around the DADA2 algorithm for analysing metabarcoding data generated through the iMapPESTS project.
There are 2 seperate workflows and vignettes available:
- Local version for analysis on windows/linux PC
- Slurm cluster version for analysis on Agriculture Victoria BASC server COMING SOON
The main workflow can be followed up with the following comparisons depending on what you are interested in
Before starting, i recommend learning about the individual componenets of the workflow:
- The indexing system we use
- The DADA2 algorithm
- The benefits of amplicon sequence variants over OTU's
- Taxonomic assignment using IDTAXA
Some other helpful tutorials include:
- DADA2 pipeline official tutorial By Benjamin Callahan.
- DADA2 example workflow by Mike Lee.