Overview of the Community Sequencing Program

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What is the Community Sequencing Program?

The Community Sequencing Program (CSP) was created to provide the scientific community at large with access to high-throughput sequencing at the Department of Energy's Joint Genome Institute (JGI) for projects of relevance to DOE missions. Sequencing projects will be chosen based on scientific merit--judged through independent peer review--and relevance to issues in global carbon cycling, alternative energy production, and bioremediation. Criteria for participation in this program, the review process, and interactions between JGI and participants are outlined on this web site. Through this program, the Department of Energy aims to advance sequence-based scientific research from a broad range of disciplines.

Two important changes for the current proposal cycle are as follows:

• The current call will be limited to whole-genome sequencing of organisms less than 200 Mb in size, pilot-scale sequencing of larger genomes, and targeted sequencing projects less than 1 Gb in size.
   
• Applications are encouraged for resequencing of organisms for which reference genomes currently exist where the proposed work will utilize new sequencing technologies (454, Solexa/Illumina platforms).

Note: A letter of intent is required to submit a proposal to the CSP. Letters for sequencing in FY2009 are no longer being accepted. The next call for proposals will be in November 2008.

How does the CSP Work?

CSP projects begin with a letter of intent from a researcher, stating that they plan to send in a proposal to sequence DNA from an organism or group of organisms. Letters of intent allow us to plan for appropriate review. The researcher then submits a proposal for consideration in the next review cycle. All proposals undergo technical review by the JGI's scientific staff, who consider feasibility and readiness to begin sequencing, checking such factors as genome size, polymorphism level, DNA quality, and the ability to make appropriate DNA libraries. Proposals are evaluated and placed in rank order by the Proposal Study Panel (PSP), a group of experts from the scientific community. The JGI Scientific Advisory Committee (SAC) then allocates proposals to the large and small genome programs based on rank and JGI sequencing capacity. Proposals become projects after they have been evaluated and project specifics agreed upon in a Scope of Work document. Work does not commence on a project until Scope of Work and User Agreement are signed and all required documents (DNA QC, sterility certification, etc.) are approved.

Once sequencing is under way, sequence traces will be released to the Genbank Trace Archive on a regular basis, in accordance with the JGI's data release policy. Interaction with applicants and others who might be interested in the project will be coordinated through the JGI's Project Management Office. At the completion of a project, the JGI will make the assemblies, gene annotations, and analyses available to the community at large. In most cases where the JGI provides more than raw sequencing reads, the JGI will also participate in the publication of the results.