S61: Characterizing genomes and transcriptomes using multi-platform next-gen sequencing approaches

The emergence of next-generation sequencing platforms has made low-cost sequencing an effective approach for tying phenotypes of industrial microbiology applications to genotype. One application of these technologies is de-novo assembly characterization of both the DNA and RNA isolates of the system. The two most widely used next-generation platforms for de novo assembly are the Illumina and Roche 454 and each system has particular strengths and weaknesses. The Illumina generates short reads (100 bp) while the Roche 454 FLX+ produces read lengths close to Sanger (800 bp), however the price per base on the Roche 454 machine is approximately 50x more costly than the Illumina platform.  Few studies exist which employ assembly of both read types, and the methods used are not explicitly described. If strategies were determined to assemble data from both platforms, and capitalize on the strengths of each system while minimizing the weaknesses and cost, researchers could apply them during future de novo assembly projects. Multi-platform de-novo assembly approaches and their application to define industrial genomes of interest are presented.