JCVI was one of three Genomic Centers for Infectious Diseases (GCID) funded by the National Institute for Allergy and Infectious Diseases (NIAID) to develop basic knowledge of infectious disease biology through the application of DNA sequencing, genotyping and comparative genome analysis. Throughout the history of GCID, and its predecessor contracts, the program has pioneered many strategies and approaches for the interrogation of genomics-based data. The program developed a suite of pipelines and tools, which are constantly updated and adapted to address new organisms, accommodate data from new sequencing platforms, and for the investigation of new types of scientific questions. All tools developed under the GCID are publicly available and open source. While JCVI is no longer funded through this NIAID funded program, the expertise and knowledge gained from it continues to flourish and enhance the greater scientific community.