The JCVI GSC will work collaboratively with NIAID and the infectious diseases research communities to provide genomic data and associated resources that will enable rational development of effective pathogen countermeasures including vaccines, therapeutics, diagnostics, and surveillance.
Below is an overview of the Center's capabilities illustrating the key components, major activities and outputs and potential impacts.
The services and capabilities, supported by the core components of the GSC are:
- Providing high throughput, high quality, and low cost genomic sequencing and genotyping services that generate a variety of publicly available genomic data for a diverse set of projects.
- Assembling and annotating genomes as well as analyzing genotyping data.
- Identifying, evaluating, and implementing new sequencing and genotyping technologies.
- Integrating data with other infectious diseases resource centers.
- Collaborating with basic and clinical infectious diseases scientists and their communities.
- Maintaining community collaborations through technical workshops.
- Educating and training infectious diseases scientists on GSC tools and methods.
Sequencing & Genotyping.
The appropriate technology and platform for each project will be selected based on the genomic diversity of the organism being studied, the organism and strains being sequenced / genotyped, and/or the scientific questions being asked. The GSC will leverage the JCVI 454 and Sanger sequencing platforms while continuing to identify, evaluate, and implement appropriate new sequencing technologies into the sequencing production pipelines. JCVI genotyping capabilities will draw on several existing genotyping platforms and assays, including Affymetrix Resequencing GeneChips®, species specific pan-genome DNA microarrays, a Molecular Inversion Probe (MIP) assay, and the SNaPshot® Assay, to complement our high throughput sequencing and PCR amplicon resequencing capabilities for efficient, cost effective, and highly accurate high throughput genotyping.
Bioinformatics GSC data generation and processing will be managed and supported by sophisticated bioinformatics systems, including a Laboratory Information Management System, automated pipelines for quality control of sequence data, genome assembly and finishing, and automated and manually-assisted annotation. Informatics tools and infrastructure also underpin the genotyping data generation and analysis pipelines. All laboratory and data analysis pipelines are modular by design, highly automated, and managed by sophisticated custom software allowing efficient handling of very large volumes of data; several of which are available as open-source tools for community use.
Open-Source Bioinformatics Tools
- Celera Assembler
- Primer Designer
- SISPA Barcode Designer
Other JCVI Web Resources