Code to analyze data from the Development and validation of an eDNA assay for detection of the endangered Franklin's bumble bee (Bombus franklini) paper

The code was used to analyze pollinator COI amplicon FASTQ sequence data in the paper titled "Development and validation of an eDNA assay for detection of the endangered Franklin’s bumble bee (Bombus franklini)" (IPDS number IP-175306, [DOI link]). The corresponding data release can be found here (IPDS number, [DOI link]). Although we use this code to analyze a pollinator COI dataset, it can be used to analyze any metabarcoding amplicon dataset.