|Genome Informatics Section
DOE Human Genome Program Contractor-Grantee Workshop
88. Informatics for Production Sequencing at LLNL
Arthur Kobayashi, David J. Ow, Matt
P. Nolan, Stephan Trong, Tory Bobo, Tom Slezak, Mark C. Wagner, T. Mimi
Yeh, Lisa Corsetti, Jane Lamerdin, Paula McCready, Evan W. Skowronski,
and Anthony V. Carrano
This past year, LLNL contributed over 8.6 MB of high-quality finished sequence to the Joint Genome Institute total of 20.9 MB. This represents an increase of more than 500% over the amount finished by LLNL last year (1.5 MB). We have managed to support this increased throughput through incremental improvements to our existing informatics infrastructure.
Our current system features extensive sample tracking, quality-control checks and reporting on every sequence run on our ABI sequencers, automated prefinishing, and an integrated suite of robotic workstations which perform rearraying, sample preps, etc. Most of our interfaces have been converted to WWW-based forms, and all of our sample information is stored in a Sybase relational database. Data is transferred through an automated sample sorting system over a dedicated 100 MB/sec ethernet local area network segment.
Over the next few years, our throughput will continue to increase at an aggressive rate. We are also faced with the challenge of relocating our core sequencing facility to Walnut Creek while developing our finishing capabilities at LLNL. We are currently working on improving our existing system through increased automation, barcode labeling of samples, and a new database schema. Some of these projects are described in more detail in other posters.
This work was performed by Lawrence Livermore National Laboratory under the auspices of the U.S. Department of Energy, Contract No. W-7405-Eng-48.
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