Scripts for in silico PCRs and output created for the comparison of short markers for DNA metabarcoding of sedimentary ancient DNA (sedaDNA).
Here, I provide the code that was used for the processing, filtering, and analysis of the markers for the paper by Zimmermann et al. Assessing the performance of short 18S rDNA markers for environmental DNA metabarcoding of marine protists. Environmental DNA (2024). DOI: 10.1002/edn3.580
The code to process the data is explained exemplary in this README and bash scripts are stored in the scripts folder of this repository. Further data processing, filtering and the analysis of the data was carried out in R. The R-scripts are part of this repository and the README guides through the order of running them.
For each marker, the folder species_lists contains a list of species that can be resolved on species level.
To run the scripts, the file marker.lineages.df.txt needs to be downloaded from GEUS Dataverse https://doi.org/10.22008/FK2/A8PSA1, where the ecoPCR output files are archived.
Run scripts in the following order:
- marker_analysis.R
- resolution_coverage.R
- barcode_resolution_coverage_supplement.R
- phylo_tree.R