Overview of the Community Sequencing Program

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 biogeochemistry. 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.

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

Proposals for bacterial and archaeal isolates will be submitted as brief white papers rather than full proposals, will be accepted on a continuous basis, and will be reviewed every three months.
The current call will be limited to whole-genome sequencing of organisms less than 250 Mb in size.
Applications are encouraged for resequencing of organisms for which reference genomes currently exist where the proposed work will utilize new short-read (Illumina) sequencing technologies.

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 JGI to plan for appropriate review and prevent full applications for projects outside of DOE mission areas. Letters are reviewed by JGI scientific staff and OBER program managers. Nearly all letters of intent are accepted for full proposal submission. The major reason for disapproval is a lack of relevance to DOE mission areas. In some cases, a meritorious project does not fit within JGI’s capabilities. In these cases, JGI scientists will often be able to suggest an alternative strategy that meets the project objectives.

Following acceptance of a letter of intent, the researcher submits a proposal for consideration in the next review cycle. All proposals undergo technical review by the JGI's scientific and technical 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. At peer review, 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 approves projects in the large and small genome programs based on rank and JGI sequencing capacity. The SAC allocation is then forwarded to DOE for final approval. Following DOE approval, project managers negotiate project specifics with PIs (including JGI scientists as needed), and the work plan is written into a Statement of Work document.

Once sequencing is under way, sequence traces are released to NCBI’s Trace Archive on a regular basis, in accordance with JGI's data release policy. Interactions with applicants and others who might be interested in the project are coordinated through JGI's Project Management Office. At the completion of a project, the JGI makes 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 also participates in publication of results.