Sunday, April 17, 2011

Interesting PLoS One paper on local assembly from short reads by "tagging" DNA via restriction enzymes

Quick one here. Interesting paper from Paul Etter et al. from Eric Johnson's lab at U. Oregon in PLoS ONE: PLoS ONE: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Here is the abstract:

"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 paired-end sequencing of restriction-site associatedDNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (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."

Note as they note in the paper "Competing interests: E.A.J. has patents filed on the RAD marker, and partial interest in a company commercializing the system. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and material" This seems like it would have potential in metagenomic applications.  I note, we are working on a similar approach - and kind of got scooped here in a way. Hope their patent does not limit what we can do.

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