Functions for cleaning up metabarcoding datasets
This package contains a set of functions I use to work with metabarcoding data output from DADA2, to remove contamination, convert dada2 sequences into easier-to-work-with sequence IDs, and generate biologist-friendly output tables.
Phyloseq objects
You can install metaclean from github with:
# install.packages("devtools")
devtools::install_github("learithe/metaclean")
metaclean requires the packages phyloseq and dplyr. It has only been tested with phyloseq version ‘1.22.3’.