The US DOE Joint Genome Institute (JGI) is a high throughput sequencing and genomic research center involved in a myriad of sequencing projects. JGI’s major effort is the sequencing of genomes and transcriptomes of plants, microbes and environmental metagenomic samples of relevance to the DOE missions of carbon sequestration, bioremediation and energy production. Roche/454’s platform utilizes emulsion PCR for template amplification and pyrosequencing technology on high well-density picotiter plate. Illumina/Solexa’s platform uses bridge amplification on glass surface for template preparation and reverse terminator technology for sequencing. Both platforms provide high throughput and high quality sequencing production at low cost, however, the read length and error distribution differ between these two significantly. Based on the different characteristics of the sequencing data, we developed, implemented and optimized various applications to best utilize the sequencing data from these two platforms. In the presentation, I am going to give examples of some of these applications such as whole genome shotgun sequencing of microbial genomes, bacterial community 16S diversity study, transcriptome sequencing (RNA-Seq), and metatranscriptome sequencing,. This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52 07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.
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