Strategies for Whole Genome, Transcriptome and Metagenomic 16S Sequencing with the Latest Next-Generation Sequencing Platforms

Next-generation DNA sequencing technologies have been widely adopted to pursue a range of important biological questions over the last several years. However, these technologies are still rapidly evolving and new platforms and procedures are introduced continuously. With the vast amount of sequencing options available, correct experimental design is crucial to project success.

Our work at the University of Illinois W. M. Keck Center for Comparative and Functional Genomics focuses on three next-generation sequencing platforms: Illumina HiSeq2000, MiSeq v2 and 454 FLX+.  We work as a Beta testing site and continuously evaluate new instrumentation and software to generate the best methods to meet the diverse research needs of the community. We have also developed and tested various methods on the MiSeq v2 (2x250bp) and the 454 FLX+ (800+ bp) platforms for long read production critical to metagenomic 16S studies, as well as de novotranscriptome and genome sequencing of eukaryotic and microbial genomes. 

Here we present results from different strategies and sequencing approaches using the very latest in next-generation sequencing platforms and software for the assembly of plant, animal and bacterial genomes. We discuss these strategies, the types of libraries used and detail their construction, as well as the costs associated with the various approaches.