Optimization of the Roche 454-Titanium GAIIx Production Sequencing Pipelines at the DOE Joint Genome Institute

Author(s): Daum, Christopher; Shapiro, Nicole; Tarver, Angela; Bauer, Diane; Swift, Bridget; Kennedy, Megan; Harmon-Smith, Miranda; Zane, Matthew; Hamilton, Matthew; Robinson, David; Cheng, Jan-Fang; Lucas, Susan | Abstract: The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Roche Genome Sequencer and Illumina Genome Analyzer pipeline has been established. Optimization of these sequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow. Primary focus has been on improving the procedural ergonomics and the technician's operating environment, reducing associated production costs, and improving the overall process and generated sequence quality. The foremost of these optimization projects, including automated 454 sample enrichment, improved 454 a Illumina sample library quantification via qPCR, and ergonomic tools, along with sequencing throughput strategies will be presented. These process improvement projects are being lead by the JGI's Process Optimization, Sequencing Technologies, Instrumentation a Engineering, and the core Roche/454 and Illumina/GA Production groups.