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 devtools package (you need to install devtools first):
devtools::install_github("fkeck/diatbarcode")This is an example which shows you how to download and load the database in R.
library(diatbarcode)
dbc <- get_diatbarcode(version = "last")
dbcYou 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