Our work at the University of Illinois W.M. Keck Center for Comparative and Functional Genomics focuses on the sequencing and assembly of eukaryotic, bacterial and archaeal genomes with the Roche/454 FLX+ and the Illumina HiSeq2000 next-generation sequencing platforms. We have tested various methods and strategies to optimize de novo whole genome and transcriptome sequencing of eukaryotic and microbial genomes, as well as for metagenomics, 16S rRNA and gene expression profiling studies.
Here we present preliminary results from different strategies for de novo sequencing of plant, animal and microbial genomes, some based primarily on 454 sequencing, some on Illumina sequencing and others utilizing a hybrid process. We discuss our assembly strategies and the types of libraries used as well as the costs associated with each sequencing approach