This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.

Public repository of data and analyses from Dirks and Jackson (2020), "Community structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy", Applied and Environmental Microbiology 86 (19)

A collection of singularity recipies for bioinformatic pipelines.

ARISE metabarcoding

Shiny app that creates files used by the OBITools to demultiplex metabarcoding sequences

Data & Code Supplement for "Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems"

Supplementary files for the paper "Environmental DNA metabarcoding of Danish soil samples reveals new insight into the hidden diversity of eutardigrades in Denmark"

Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow

Supplementary files for Ribeiro et al. ISME 2018

eDNA pipeline showcase

Datasets and code used to create figures in "Hajibabaei et al., 2019. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk tissue biomonitoring samples. PLoS ONE 14(12): e0225409."

Metabarcoding analysis pipeline, using DADA2 and qiime2

A primary goal of this research was to characterize vent plume biogeography across a spatial gradient. This study was done in collaboration with OceanX during the 2021 Young Explorers Program.

Code that was used to generate figures for the Mahmoudi et al., 2013 publication

Master 1 project of 4 students at Institut Agro Montpellier in collaboration with a research lab for population biology and management (CBGP) in Montpellier

taxalogue - a toolkit to create comprehensive CO1 reference databases

A tool to select the best primers to perform quantitative metabarcoding studies.

COI sequences files used to test the COI Classifier Web Portal

CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing