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The ATCC® Genome Portal - Authenticated Microbial Reference Genomes with Data Provenance

Blue DNA strand with sides made of light blue balls.

Bio-IT World Conference & Expo

Boston, Massachusetts, United States

May 16, 2023


Publicly available microbial genomes are commonly used in industry research for a variety of purposes. These data, however, are often poor quality or lack critical metadata, which can lead to delays in research progress and increased costs.

In response, we created the ATCC® Genome Portal: a regularly updated database of de novo genome assemblies and annotations for microbes held in the ATCC collection. Currently, the ATCC Genome Portal includes 3,118 genome assemblies produced in-house by ATCC from materials sourced directly from our biorepository. The database currently provides references for 2,679 bacteria, 243 viruses, 192 fungi, and 4 protists—including genome assemblies for 1,007 type-strains. The content of the ATCC Genome Portal is updated every month with new genome assemblies, and we aim to reach 10,000 authenticated genomes by 2025. Here, we describe our standardized workflows, data diversity, and recent comparative genomics highlights from the genome portal.

Each bacterium, fungus, and protist is sequenced on both Illumina and Oxford Nanopore platforms; the results of which are used to produce hybrid de novo assemblies for each strain. Viruses are currently sequenced using only Illumina sequencing. Each assembly on the ATCC Genome Portal includes metrics for sequencing quality, assembly completeness, genome annotations, and metadata such as antibiotic susceptibility, isolation data, origins, and phenotypic data.

The ATCC Genome Portal and the data contained therein is available for research-use and is accessible via the web or via a new REST-API. Please visit for details.


Download the poster to learn about our bioinformatics pipelines for generating reference-quality genomes



Jonathan Jacobs, headshot.

Jonathan Jacobs, PhD

Senior Director of Bioinformatics, ATCC

Dr. Jonathan Jacobs leads ATCC’s Sequencing & Bioinformatics Center and the development of the ATCC Genome Portal. He has over 20 years of experience in molecular genetics, bioinformatics, and microbial genomics, and he has worked throughout his career at the interface of academia, government, and industry. He holds a joint Research Professor appointment at Syracuse University’s Forensic & National Security Sciences Institute in support of microbial forensics graduate student training and research, and he actively collaborates with several US public health laboratories involved in pathogen genomics research and surveillance. Dr. Jacobs is also certified in Product Management from Pragmatic Institute, and he has led successful commercial launches of several bioinformatics products into the market.

DNA rods with bacteria.

Reference-quality sequences

Through the ATCC Genome Portal, you can easily search, access, and analyze thousands of reference-quality genome sequences. Our optimized methodology is designed to achieve complete, circularized (when biologically appropriate), and contiguous genomic elements by using short-read (virology collection) and hybrid (bacteriology, mycology, and protistology collections) assembly techniques. We then take our workflow one step further by accompanying each stage of the process with rigorous quality control analyses that ensure the highest quality data. Only the data that passes all quality control criteria are published to the ATCC Genome Portal. Visit the portal today to find the high-quality data you need for your research.

Visit the portal