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Access the diat.barcode database with R
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README.md
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README.md

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diatbarcode

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:

Installation

You can install the package diatbarcode from GitHub with the devtools package (you need to install devtools first):

devtools::install_github("fkeck/diatbarcode")

Example

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
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