RAD_PE_contigs

Despite the power of massively parallel sequencing platforms, de novo assembly with the short reads produced remains difficult. We demonstrate that short reads can be locally assembled into larger contigs using paired-end sequencing of restriction-site associated DNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. RAD-PE contigs mitigate the problem of short reads by creating much longer high-quality contigs appropriate for SNP discovery or the de novo assembly of genomes.