tidyGenR: tidy multilocus amplicon genotypes in R

Multiplexed amplicon sequencing has become an important tool in phylogenetics and conservation genetics. Amplicon sequencing reads need to be processed to get final haplotypes. The bioinformatics involved is often limiting for embarking on these kind of projects and there are few tools designed to handle this type of data. tidyGenR is an R package for reproducible multilocus amplicon genotyping workflows from sequencing reads. It provides a modular workflow that starts by demultiplexing loci, variant determination with DADA2, and ends with genotyping. Input data can be raw single-end or paired-end FASTQ reads and the main outputs are haplotypes in tidy tables. Results can also be exported as FASTA files. We successfully tested tidyGenR on amplicon libraries of 27 loci from a population genetics study in a rodent. The results from tidyGenR were reliable and robust across a wide range of read depths. In addition, tidyGenR offers greater flexibility and interoperability.