Sequencing Department
The Sequencing Department aims always to generate high-quality sequence in a cost-efficient manner. Its activities follow the DNA from library creation, through sequencing prep, to capillary sequencing and analysis. As genomics is a rapidly changing field, the department constantly adapts to take best advantage of new developments in technology. The current stable of sequencing machines comprises 70 Applied Biosystems ABI 3730xl's running 24/7, two Roche 454 GS-FLX pyrosequencers, and two Solexa pyrosequencers. All our protocols are available on the Protocols in Production Sequencing page.
Groups
Process Optimization
The Process Optimization Group has three main functions: (1) to increase production efficiency, data quality, and reduce costs through improving the library construction and sequencing processes; (2) to serve as a pilot group to test out new production processes and ensure a smooth transition into the production operations; and (3) to develop new production pipelines to enhance the JGI sequencing capability. This group also works with other support teams to analyze problems that arise in the production sequencing process and provides solutions. The Cloning Technology subgroup constructs all the libraries sequenced at JGI.
Group lead: Jan-Fang Cheng
Quality Assurance/Quality Control
The Quality Control Group checks all reagents used in production sequencing and runs the capillary sequencers.
Project/Freezer Management
This group handles project management for production sequencing, representing the production line in the Project Management Office. The group also ensures that samples are stored and tracked correctly as they pass through production sequencing.
Instrumentation
The Instrumentation Group is responsible for the upkeep and preventative maintenance of all the instruments in the production line.
Instrumentation Group web site
Production Shifts
Preparation of DNA for sequencing and the sequencing process itself are carried out by technicians in an AM shift and a PM shift. Their efforts are guided by the Production Coordinator.
454
The 454 group performs sequencing with the Roche 454 GS-FLX system. The members are working to optimize the process of pyrosequencing at JGI and integrate it into the JGI production sequencing pipeline.
Microbial Genomics
The Microbial Genomics group is responsible for integration of new sequencing technologies into microbial genome assembly and finishing. The group is focused on finishing special microbial and metagenomic projects and developing new tools and approaches for finishing process improvement.
