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. These process improvement projects are being lead by the JGI's Process Optimization, Sequencing Technologies, Instrumentation and Engineering, and the core Roche/454 and Illumina/GA Production groups. Primary focus has been on improving the procedural ergonomics and the technician's operating environment, reducing manually intensive technician operations with tools and robotic automation, reducing associated production costs, and improving the overall process and generated sequence quality. The foremost of these optimization projects, along with sequencing strategies, throughput numbers, and sequencing quality results will be presented.