eDNA sequence data and analyses comparing filtration methods and extraction protocols for biomonitoring of vertebrate taxa
Raw sequences are deposited in the National Center for Biotechnology Information’s Sequence Read Archive (BioProject: PRJNA1541148).
├── data/
│ ├── raw/ # Metadata and eDNA read table output from Apscale_Nanopore
│ └── processed/ # Decontaminated OTU tables, long-format data, resulting tables from ordination analyses
├── results/
│ ├── figures/ # Figures for manuscript and analyses
│ ├── tables/ # Table results: upset plot
├── mibird diversity analysis.Rmd
├── teleo diversity analysis.Rmd
├── combined diversity analysis.Rmd
├── upset_method.Rmd
└── README.md
| Step | File | Description |
|---|---|---|
| 1 | mibird diversity analysis.Rmd | imports MiBird otu table, filters samples, decontaminates with microDecon, runs community analysis |
| 2 | teleo diversity analysis.Rmd | imports Tele02 otu table, filters samples, decontaminates with microDecon, runs community analysis |
| 3 | combined diversity analysis.Rmd | produces main text figures with combined results from both MiBird and Tele02 datasets |
| 4 | upset_method.Rmd | runs UpSet analysis and produces method-specific UpSet plot |
Please cite the associated manuscript when using these data.
Patrick Nichols
Postdoctoral Researcher
Biodiversity Genomics Research Group
University of Oulu
📧 patrick.nichols@oulu.fi
🔗 https://biodiversitygenomics.org/