The goal of the diatbarcode is to download the database Diat.barcode locally, in order to use it directly within the R environment.
The diat.barcode database is a library of barcodes for diatoms and other algae which is curated and which guarantees good taxonomical homogeneity and good quality of sequences.
More information on the diatbarcode website:
You can install the package
diatbarcode from GitHub with the
remotes package (you need to install
This is an example which shows you how to download and load the database in R.
library(diatbarcode) dbc <- get_diatbarcode(version = "last") dbc
You can also use the function
download_diatbarcode to download the database in a given location on your computer. The function allows to download different flavors of the original database. For example,
download_diatbarcode is particularly useful to quickly download a pre-formated reference database for taxonomic affiliation with DADA2 (
flavor = "rbcl312_dada2_tax"). See our DADA2 pipeline for an example.
library(diatbarcode) # By default the file is saved in the temporary directory dbc_dl <- download_diatbarcode(flavor = "rbcl312_dada2_spe") # The function returns the path where the file was saved and other infos silently dbc_dl