eDNA metabarcoding pipeline

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

Tool repositiory for bam files

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

R package for fitting Bayesian multiscale occupancy models

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

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

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.

Offline-first PWA for logging environmental DNA sample metadata with Darwin Core and FAIR-compliant exports.

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.

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

Burrow-Wheeler Aligner for short-read alignment (optimized for aeDNA)