Amplicon Sequencing (AmpSeq) is a practical, intuitive strategy with a semi-automated computational pipeline for analysis of highly multiplexed PCR-derived sequences. Amplicons can target from a single nucleotide to the upper limit of the sequencing platform. The flexibility of AmpSeq’s wet lab methods make it a tool of broad interest for diverse species, and AmpSeq excels in flexibility, high-throughput, low-cost, accuracy, and semi-automated analysis. Here we describe the procedure to output data out of an AmpSeq project, with emphasis on the bioinformatics pipeline to generate SNPs, haplotypes and presence/absence variants in a set of diverse genotypes.

Publishes in Frontiers in Plant Sciences as Computational Analysis of AmpSeq Data for Targeted, High-Throughput Genotyping of Amplicons