maine-edna / medna-metadata

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

Maine-eDNA Metabarcoding Tutorial

This self-guided workflow tutorial will cover analysis of Illumina MiSeq data from initial reads to amplicon sequence variants (ASVs), taxonomy, and visualization. The workflow uses data generated by Maine-eDNA researchers for 18S using the Comeau et al., 2011 primers E572F/E1009R for the V4 region. A containerized environment was created in CyVerse for software setup, which uses FastQC, Cutadapt, and R packages for analysis and visualization {Dada2, Phyloseq, GGplot2}.

For more information on using CyVerse, see the help documentation here.

Suggested Publications

• Bohmann et al. 2014 - Environmental DNA for wildlife biology and biodiversity monitoring. TREE, 29.
• Schnell et al. 2015 - Tag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies. Molecular Ecology Resources, 15, 1289-1303.
• Callahan et al. 2016 - DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583.
• Ficetola et al. 2016 - How to limit false positives in environmental DNA and metabarcoding? Molecular Ecology, 16, 604-607.
• Callahan et al. 2017 - Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J, 11, 2639–2643.
• Deiner et al. 2017 - Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26, 5872-5895.
• Alberdi et al. 2017 - Scrutinizing key steps for reliable metabarcoding of environmental samples. Methods in Ecology and Evolution, 9, 134-147.
• Dickie et al. 2018 - Towards robust and repeatable sampling methods in eDNA-based studies. Molecular Ecology Resources, 18, 940-952.
• Lamb et al. 2019 - How quantitative is metabarcoding: A meta‐analytical approach. Molecular Ecology, 28, 420-430. -Jamy et al. 2019. Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity. Molecular Ecology Resources, 20, 429-443.
• Zinger et al. 2019 - DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology, 28, 1857-1862
• Antich et al. 2021 - To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics, 22,177.