GCID Cores

The long-range objective of the J. Craig Venter Institute (JCVI) Genomic Center for Infectious Diseases (GCID) is to develop basic knowledge of infectious disease biology through the application of genomic technologies. JCVI has been engaged in this research field since our founding in 1992. The Program is based on the application of innovative genomics-based approaches to study pathogens and determinants of their virulence, drug-resistance, immune-evasion and interactions with the host, and interactions with the host microbiome. The Program builds on our experience as an NIAID Microbial Sequencing Center (MSC) and Genomic Sequencing Center for Infectious Diseases (GSCID).

Core Leaders

Core A: Administration

Dr. Karen E. Nelson; President of JCVI

Dr. William Nierman; Professor, Infectious Diseases

Core B: Technology

Dr. Granger Sutton; Professor, Project Director

Core C: DMARD

Dr. Granger Sutton; Professor, Project Director

GCID Activities

Below is an overview of the Center's capabilities illustrating the key components, major activities and outputs and potential impacts.

Technology Core, and the Data Management, Analysis and Resources Dissemination (DMARD) Cores

The Center is supported by the Technology Core, and the Data Management, Analysis and Resources Dissemination (DMARD) Cores which:

  • Provide 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.
  • Assemble and annotate genomes as well as analyzing genotype data.
  • Identify, evaluate, and implement new sequencing and genotyping technologies.
  • Integrate data with other infectious diseases resource centers.
  • Collaborate with basic and clinical infectious diseases scientists and their communities.
  • Maintain community collaborations through technical workshops.
  • Educate and train infectious diseases scientists on GCID tools and methods.

Sequencing

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 GCID will leverage a combination of MiSeq, NextSeq, HiSeq, IonTorrent, PacBio and MiniION Oxford Nanopore sequencing platforms while continuing to identify, evaluate, and implement appropriate new sequencing technologies into the sequencing production pipelines.

Bioinformatics

GCID data generation and processing is managed and supported by a 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. In addition, the ontologies based metadata tracking system (O-META) has been enhanced. 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. The DMARD Core releases tools and pipelines under an open source plan to the community according to NIAID data sharing and release guidelines.

Open-Source Bioinformatics Tools