A simple bead-based method for generating cost-effective co-barcoded sequence reads

Abstract

Advances in genome sequencing continue to decrease cost and improve quality. However, the diploid information found in most genomes is still lost by the most common sequencing methods. There are several methods currently available for obtaining this haplotype information. However, most of these methods are either time consuming, require expensive equipment and reagents, or both. Here we describe single tube long fragment read (stLFR), a simple barcoded bead-based process capable of near perfect whole genome variant calling and haplotyping. Our method uses equipment available in nearly all molecular biology laboratories and costs approximately 30 dollars a sample. In addition, the data generated from this process is capable of detecting and phasing structural variations and scaffolding contigs. We expect in the future that this process will enable affordable diploid de novo assembly.