This is a simple pipeline for analysing metabarcoding data. It strings together functions provided in several packages and can be used for the analysis of eDNA metabarcoding data.
The pipeline has been tested on Ubuntu/Debian and Mac OS 10.14 onwards and (depending on the functions used) requires the following software packages.
- Install above dependancies
- Launch R
install.packages("devtools")
library("devtools")
install_github("leholman/metabarTOAD")
library("metabarTOAD")
You can read an overview of the pipeline using the UPARSE/UNOISE algorithm here, and DADA2 here.