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Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using  p aired- e nd sequencing of  r estriction-site  a ssociated  D NA (RAD-PE) fragments. We use this RAD-PE contig approach to identify  s ingle  n ucleotide  p olymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence  E. coli  and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long.

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads