Header

UZH-Logo

Maintenance Infos

Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb


Keck, François; Altermatt, Florian (2023). Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb. Molecular Ecology Resources, 23(2):511-518.

Abstract

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.

Abstract

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.

Statistics

Citations

Dimensions.ai Metrics
3 citations in Web of Science®
6 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

4 downloads since deposited on 09 Dec 2022
1 download since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Global Change and Biodiversity
Dewey Decimal Classification:570 Life sciences; biology
Scopus Subject Areas:Life Sciences > Biotechnology
Life Sciences > Ecology, Evolution, Behavior and Systematics
Life Sciences > Genetics
Uncontrolled Keywords:barcoding, DNA reference library, metabarcoding, R package, reference database
Language:English
Date:1 February 2023
Deposited On:09 Dec 2022 15:03
Last Modified:01 Feb 2024 01:01
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:1755-0998
OA Status:Green
Publisher DOI:https://doi.org/10.1111/1755-0998.13723
Project Information: