environmental-dna

eDNA metabarcoding pipeline

An open-source data management system for tracking environmental DNA samples and metadata

Tool repositiory for bam files

AI-powered eDNA classification platform using Nucleotide Transformer for marine biodiversity analysis - taxonomic classification, novelty detection, interactive mapping & rich analytics

R package for fitting Bayesian multiscale occupancy models

This repository contains scripts and data for training and utilizing machine learning classifiers to predict qPCR cross-amplification.

Scripts for executing a filtering, clustering and identification pipeline for eDNA samples.

Calculate optimal combination of eDNA barcodes based on amplicon sequences

Comparison between eDNA and trawling for fish biodiversity metrics

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

A web tool for optimally choosing eDNA primer pairs to identify a set of taxa.

Detect novel bacterial taxa in metagenomic data using ANI-weighted placement uncertainty. Distinguishes true novelty from taxonomic ambiguity by combining competitive read recruitment with genome-genome ANI matrices. Species/genus classification with literature-backed thresholds.

Tool for matching taxonomy tables against GBIF, with browser and command-line workflows.

Hierarchical Bayesian occupancy modeling across four biodiversity survey methods (camera traps, water/soil eDNA, iDNA) — Unini Extractive Reserve, Amazon

https://isrudev.github.io/eDNABook/ Offline-first PWA for logging environmental DNA sample metadata with Darwin Core and FAIR-compliant exports.

Nextflow DSL2 pipeline for Oxford Nanopore eDNA metabarcoding: isONclust clustering, racon/medaka consensus, and BLAST taxonomy that flags no-hit/low-identity sequences instead of dropping them. Modern decona replacement.

Taxonomic classification of DNA sequences using BLAST or vsearch with configurable identity thresholds and batch processing

Reproducible environmental DNA (eDNA) analysis platform. Turns raw FASTQ reads into real ASVs, taxonomy (SILVA, MIDORI2), conservation status (GBIF, IUCN Red List), and diversity metrics, with signed provenance manifests and GBIF-ready exports (Darwin Core, BIOM). FastAPI plus React. No mock data.