Our lab has pioneered the use of whole genome sequencing (WGS) to pinpoint mutagen-induced molecular lesions, thereby shortcutting time-consuming positional cloning. This review highlights the promise we see for WGS:
The Impact of Whole Genome Sequencing on Model System Genetics: Get Ready for the Ride, Hobert O. Genetics. 2010 Feb;184(2):317-9.
CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O. Genetics. 2012 Dec;192(4):1249-69.
CloudMap has superseded MAQGene, our earlier software for mutant genome sequence analysis (we no longer support MAQGene):
MAQGene: software to facilitate C. elegans mutant genome sequence analysis. Bigelow H, Doitsidou M, Sarin S, Hobert O. Nat Methods. 2009 Aug;6(8):549.
Our whole genome sequencing sample prep is available here. NEW UPDATE 7/9/2013: we now recommend that phenol extraction should be avoided.