genner-lab/tilapia-aquaculture-edna

Code and data for manuscript on monitoring Tanzania tilapia aquaculture using eDNA # Tilapia Aquaculture eDNA Collins RA, Saxon AD, Shechonge AH, Kishe MA, Ngatunga BP & Genner MJ. (2026). Environmental DNA-based quantification of an invasive tilapia species in Tanzanian inland aquaculture. _Aquaculture, Fish and Fisheries_ doi.org. Code and data for article on monitoring Tanzania tilapia aquaculture using eDNA. ### Download data and install R packages ```bash # clone the repository onto your local machine git clone github.com cd tilapia-aquaculture-edna mkdir temp # install R packages - requires R v4.4.1 Rscript -e "renv::restore()" ``` ### Process qPCR ```bash # run scripts to generate tables and figures scripts/qpcr.R scripts/models.R scripts/haplotyping.R scripts/primer-efficiency.sh ``` ### Repository contents * **`data/`** - Raw and processed data used in analyses. - `Ciezarek_MtDNA_GenomicAncestry_Correspondence.txt` - data from Ciezarek et al. studies - `events-master.csv` - table of eDNA sampling events - `extractions-master.csv` - table of eDNA extractions and metadata - `nd1-metadata.csv` - metadata describing all ND1 sequences used - `qpcr-results.csv` - raw data from qPCR analyses - `sra-nd1-references.fasta` - ND1 reference sequences obtained from SRA - `tilapia-ml-tree.nwk` - phylogenetic tree used for ND1 haplotyping - `tissues.fasta` - FASTA file containing nucleotide data from sequenced tissue samples - `tissues-master.csv` - table containing metadata from tissue samples * **`renv/`** - Settings for the R environment. * **`scripts/`** - R scripts to run analyses. - `genbank-submit.R` - script to generate and check files to submit to GenBank - `haplotyping.R` -script to identify haplotyped individuals - `load-libs.R` - script to load package libraries and custom functions - `models.R` - script to run site occupancy models - `primer-efficiency.R` - script to estimate potential off-target primer binding - `primer-efficiency.sh` - script to estimate p …