GAPeDNA
Interactive tool for investigating coverage gaps in eDNA metabarcoding reference databases for marine, freshwater, and elasmobranch fish species
Install / Use
/learn @virginiemarques/GAPeDNAREADME
GAPeDNA
GAPeDNA is an interactive web application for exploring taxonomic coverage gaps in eDNA metabarcoding reference databases. For a given primer pair and taxonomic group, it maps the proportion of species represented in the reference database across spatial regions worldwide.
🌐 Live app: shiny.cefe.cnrs.fr/GAPeDNA
If the link is unavailable, the server may be under maintenance (typically resolved within a few days). Please open an issue if the outage persists.
Overview
Reference sequences can now be recovered even in the absence of the primer binding sites by in silico PCR. GAPeDNA accounts for up to 3 mismatches per primer.
The database is updated periodically. Current version: MIDORI2 GenBank 269 (2025-12-09).
Features
- Interactive choropleth maps — visualise per-region primer coverage as a percentage of species with a reference sequence
- Species table — click any polygon to display the full species list for that region, including IUCN conservation status and sequencing status for the selected marker
- Sequence extraction — upload a downloaded species table to retrieve the corresponding reference sequences and per-primer mismatch counts
- Download — export species tables and sequence data as CSV
Taxonomic groups & spatial resolutions
| Group | Spatial resolutions | Checklist source | |---|---|---| | Marine fish | Ecoregions, Provinces, World | Albouy et al. 2019 | | Freshwater fish | Drainage basins, World | Tedesco et al. 2017 | | Elasmobranchs (sharks & rays) | Ecoregions, Provinces, Basins, World | IUCN Red List spatial data |
How to use the app
World maps pane
- Choose a taxon — marine fish, freshwater fish, or elasmobranchs
- Choose a spatial resolution — available options update automatically based on the taxon
- Choose a mitochondrial marker position — 12S, 16S, COI, CytB, or 18S
- Choose a primer pair — the interactive map renders immediately
Hover over any polygon to display the percentage of species sequenced. Click a polygon to load the full species list in the table below, with IUCN status and sequencing status per species. The table supports filtering and sorting. Use the Download button to export it as CSV.
Sequence extraction pane
Upload a CSV file exported from the World maps pane. The app will join each species to its reference sequence for the corresponding marker and display per-primer mismatch counts. The full table (including complete sequences) can be downloaded.
Demonstration
Run locally
You need R (≥ 4.1) with the following packages installed:
shiny, leaflet, sf, dplyr, DT, htmltools, shinythemes, shinycssloaders
Option 1 — directly from GitHub:
library(shiny)
runGitHub("GAPeDNA", "virginiemarques")
Option 2 — clone and run:
git clone https://github.com/virginiemarques/GAPeDNA
cd GAPeDNA
library(shiny)
runApp()
The
data/data_for_GAPeDNA.Rdatafile (~100 MB) is not included in the repository. It is generated by the companion pipeline inGenerate_data_GAPeDNAor available on request.
Contributing
Contributions to expand GAPeDNA's taxonomic scope are welcome. To propose a new group, please open an issue labelled enhancement and provide:
- One or more primer pairs targeting the group
- A global, spatialised species checklist at an appropriate resolution
Citation
If you use GAPeDNA in your work, please cite:
Marques V. et al. (2021). GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding. Diversity and Distributions, 27, 1142–1155. https://doi.org/10.1111/ddi.13142
Credits
- Development & maintenance: Virginie Marques
- Illustration: P. Lopez (UMR MARBEC)
- Server deployment: A. Granier (CEFE)
- In silico PCR: CRABS
License
MIT © Virginie Marques — see LICENSE for details.
