Amplicon sequencing analysis workflow using DADA2 and QIIME2

This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies

This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.

Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)

unofficial Edna Mall showtime API

A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.

eDNA pipeline

Data processing workflow and supplementary data for Li et al. 2019 - Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes

Community Matrix Analysis

eDNA pipeline showcase

Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)

repository of data examples for the R package metabaR

A collection of singularity recipies for bioinformatic pipelines.

website of the otterconnect project

Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)