QTLseqr: An R package for bulk segregant analysis with next-generation sequencing

Abstract

Next Generation Sequencing Bulk Segregant Analysis (NGS-BSA) is efficient in detecting quantitative trait loci (QTL). Despite the popularity of NGS-BSA and the R statistical platform, no R packages are currently available for NGS-BSA. We present QTLseqr, an R package for NGS-BSA that identifies QTL using two statistical approaches: QTL-seq and G'. These approaches use a simulation method and a tricube smoothed G statistic, respectively, to identify and assess statistical significance of QTL. QTLseqr, can import and filter SNP data, calculate SNP distributions, relative allele frequencies, G' values, and log10(p-values), enabling identification and plotting of QTL. The source code is available at https://github.com/bmansfeld/QTLseqr