The FASTA files are downloaded from the eurofins website and run using BLAST to classify the species from the CytB sequence. The protocol for the setup of the BLAST algorithm is available in the Chapter 3 repository here.

The sequencing.csv file is manually updated with the results of the BLAST search and is stored in the data/inventory folder.

The sequencing_results.R script can then be run to pull in additional data on the samples from the rodent_trapping repository.

An updated list of the samples remaining to be sequenced can be generated once this is run. The to_be_sequenced.R script requires an updated sequencing.csv to compare available samples with those that have been successfully analysed.