Gulf eDNA Network
Mapping Species across the Gulf
Resources for eDNA research
Sampling Protocols
Environmental DNA Sampling Protocol – Filtering Water to Capture DNA from Aquatic Organisms, Lamarine et al. 2025
eDNA Sampling Protocols and Videos
‘Omics Program Protocols
Laboratory Analysis
Primer sequences for a variety of taxa used at HCGS
A manager’s guide to using eDNA metabarcoding in marine ecosystems
Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. PeerJ. 2022.
‘Omics Program Protocols
Guidance on the use of targeted environmental DNA (eDNA) analysis for the management of aquatic invasive seqcies and species at risk. Abbott et al. 2022
Molecular Data Analysis Tools
Metabarcoding
Bioinformatic Methods for Biodiversity Metabarcoding
Creedy, Volger, & Penlington
Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data
Dominik Buchner
‘Omics Program Protocols
DADA2: High resultion sample inference from Illumina amplicon data
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. Nat Methods. 2016
16S Metabarcoding with Qiime2
Joseph Sevigney
Resources for microbial metabarcoding
Taxonomy and Phylogenetics
SHOOT.bio
Phylogenetic search engine
galaxy-tool-lca
A tool to determine the lowest common ancestor from BLAST results with taxonomy. This approach is partly based on MEGAN’s (Huson et al., 2007) LCA method.
EBBS: Error based BLAST Sequence Filter
Smithsonian Museum of Natural History
Tutorials
DADA2 Pipeline Tutorial
Qiime 2 View
Visualizing Qiime2
BASH Tutorial Joseph Sevigney
Glitter
Git repositories with educational materials for computational life sciences
Geneious Academy
Molecular biology and bioinformatics courses
Bioinformatic Tutorials and Resources
R Packages
rBLAST
R Interface for the Basic Local Alignment Search Tool
taxize
Gathers taxonomic information from around the web
phytools
A wide range of phylogenetic tools for comparative biology
abbagadabba
Amplicon and region-based biodiversity assessment, gap analysis, and database building
referee
Scripts for building reference databases, and species list cleaning
mednaTaxaRef
Reference databases for Maine eDNA sequence analyses
BOLDConnectR
Interactive data access on BOLD
insect
Tool to assign taxon identifications to amplicon libraries using informatic sequence classification trees
Other eDNA Resource Lists
eDNA Resources
Wilder Lab
Genomics & eDNA
‘Omics Program
