Integrated reanalysis of global riverine fish eDNA datasets

Environmental DNA (eDNA) has revolutionized biodiversity monitoring in aquatic ecosystems. One of its possible hallmarks is the potential global comparability of datasets, yet this opportunity has been largely left unexplored due to diverse sampling protocols and bioinformatic workflows. This dataset compiles and harmonizes riverine fish community data derived from environmental DNA (eDNA) metabarcoding studies conducted worldwide. In total, this dataset comprises 58 riverine fish eDNA metabarcoding datasets from 1,818 sampling sites, comprising both published and novel datasets with the goal of assessing and comparing biodiversity patterns from the individual original studies with a unified analysis under a common bioinformatic pipeline. We thereby demonstrate the power of integrating individual eDNA metabarcoding datasets for biodiversity assessment and monitoring.
, , # Integrated reanalysis of global riverine fish eDNA datasets

Project leaders:

* Florian Altermatt (University of Zurich, Switzerland)
* Xiaowei Zhang (Nanjing University, China)
* Loïc Pellissier (ETH Zurich, Switzerland)
* Yan Zhang (Nanjing University, China)

README version date:
20 April 2026

## 1. General description of the archive

This archive contains metadata, raw sequencing datasets, reformatted eDNA datasets, and unified downstream analysis outputs used in the project “Integrated reanalysis of global riverine fish eDNA datasets”.

The archive includes:

* archive-level metadata and dataset crosswalk files
* raw sequencing datasets
* standardized reformatted datasets
* outputs from unified downstream analyses of raw sequencing data

## 2. Archive contents

This archive includes the following main components:

### `1_Info.zip`

Archive-level metadata and dataset crosswalk files.

Contents:

* `AllDataTableCheckList.csv`: metadata checklist for all reformatted datasets, iden..., ,