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refdb: A reference database manager for R

The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export reference genetic data. It has been designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in metabarcoding studies.

Installation

You can install the development version of refdb from GitHub.

remotes::install_github("fkeck/refdb")

Find more about the package (manual, vignettes, etc.): https://fkeck.github.io/refdb/

Citation

If you use the refdb package in your work, please cite:

Keck, F., & Altermatt, F. (2023). Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb. Molecular Ecology Resources, 23(2), 511-518. https://doi.org/10.1111/1755-0998.13723.

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Version

Install

install.packages('refdb')

Monthly Downloads

243

Version

0.1.2

License

GPL-3

Maintainer

Francois Keck

Last Published

December 19th, 2025

Functions in refdb (0.1.2)

refdb_clean_tax_remove_extra

Remove extra words from taxonomic names

refdb_export_dada2

Export reference database for DADA2

refdb_clean_seq_remove_gaps

Remove gaps from genetic sequences

refdb_clean_tax_harmonize_nomenclature

Harmonize taxonomic name nomenclature

refdb_clean_tax_NA

Convert missing taxonomic names to NA

refdb_check_seq_homogeneity

Check for genetic homogeneity of taxa

refdb_check_tax_typo

Check for typos in taxonomic names

refdb_check_tax_conflict

Check for conflicts in taxonomy

refdb_clean_seq_remove_sideN

Remove repeated side N from genetic sequences

refdb_clean_seq_crop_primers

Crop genetic sequences with a set of primers

refdb_filter_seq_stopcodon

Filter sequences based on their number of of stop codons.

refdb_filter_seq_length

Filter sequences based on their number of character.

refdb_fill_tax_downstream

Fill missing data in taxonomy

refdb_clean_tax_remove_subsp

Remove subspecific information from taxonomic names

refdb_import_NCBI

Download and import NCBI Nucleotide records

refdb_filter_seq_homopolymers

Filter sequences based on their number of repeated character.

refdb_export_idtaxa

Export reference database for DECIPHER (IDTAXA)

refdb_filter_seq_duplicates

Filter duplicated sequences.

refdb_filter_tax_na

Filter records NA taxa

refdb_filter_ref_scope

Filter records by taxonomic scope of studies

refdb_filter_seq_primer

Filter sequences based on the presence of primers.

refdb_filter_seq_ambiguous

Filter sequences based on their number of ambiguous character.

refdb_filter_tax_precision

Filter records based on their taxonomic precision.

refdb_set_ncbitax

Replace the current taxonomy using the NCBI Taxonomy database

refdb_sample_tax

Sample records within taxa

refdb_write_fields

Write fields to a file

refdb_plot_tax_barplot

Barplots of the number of records for the most represented taxa

refdb_set_fields

Associate columns to fields

refdb_get_fields

Get fields of a reference database

refdb_plot_seqlen_hist

Plot an histogram of sequence lengths

Plot an interactive map

refdb_plot_tax_treemap

Reference database treemap

Compile a report with different checks

Merge reference databases

refdb_plot_tax_tree

Reference database taxonomy tree

valid_taxo_rank

Ranks considered as valid by refdb

Extract XML elements

process_geo_ncbi

Process coordinate column returned by NCBI

Taxonomic ranks of the NCBI Taxonomy database

igraph_from_taxo

Create a graph from a taxonomic table

Internal check for fields

Functions to set fields for various databases

refdb_check_seq_conflict

Check for conflicts in sequences

make_ncbi_table

Parse NCBI XML and make a table

refdb_clean_tax_remove_blank

Remove blank characters from taxonomic names

Scores for filtering operations

get_ncbi_taxonomy

Get NCBI taxonomy

refdb: A DNA Reference Library Manager

refdb_clean_tax_remove_uncertainty

Remove terms indicating uncertainty in taxonomic names

refdb_export_utax

Export reference database for USEARCH/VSEARCH

refdb_export_mothur

Export reference database for Mothur

refdb_fill_tax_upstream

Fill missing data in taxonomy