This repository (R project) contains all data and scripts necessary to run the analyses and produce the figures from the study Man against machine: Do fungal fruitbodies and eDNA metabarcoding give similar biodiversity assessments across broad environmental gradients?. (Frøslev et al. (2019) - published in Biological Conservation).
All steps/processes for this study can be carried out on the same computer/platform. But, in practise all analyses were carried out on a linux server setup with 64 processors (AMD Opteron(tm) 6380), except R-scripts, which were run on a MacBook Pro (2.9 GHz Intel Core i7, 16 GB 2133 MHz LPDDR3).
All analyses were carried out in one directory and sub-directories of this.
The Illumina sequence data is deposited here: https://sid.erda.dk/public/archives/b0d2b22cb7804ff23d1612f4afdc29ae/published-archive.html
- VSEARCH v.2.9 (or later) (https://github.com/torognes/vsearch)
- Cutadapt v 1.17 (https://cutadapt.readthedocs.io/en/stable/)
- blastn v2.4.0+ (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
Various R-packages were used for this study (see in the relevant markdown files).
- in_data : contains all initial data not produced as part of the analyses here
- data : contains all the data produced as part of the analyses here
- seq_processing : contains all the scripts and files necessary to perform the initial sequence processing
- tables : output directory for (text) tables produced in the analyses
- R : contains a few functions used in the analyses
- plots : output directory for the plots/figures produced in the analyses
Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Hansen, A. J., Læssøe, T., & Heilmann-Clausen, J. (2019). Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?. Biological Conservation, 233, 201-212. https://doi.org/10.1016/j.biocon.2019.02.038