• Quick Order
  • Careers
  • Support

Does Long-Read Sequencing Technology Produce Superior Viral Genome Assemblies?


ASM Microbe 2024

Atlanta, Georgia, United States

June 14, 2024


ATCC provides a growing portfolio of clinically relevant viral strains that are used in a variety of research areas like drug discovery and therapeutic development. While the genomes for many of these viruses are available in public databases, we have shown that the referenced genomes published by third parties are often error prone, incomplete, or generated using a variety of methods, which makes the downstream use of the data challenging. To address this problem, we developed reproducible next-generation sequencing and genome assembly workflows to produce viral assemblies for over three hundred viruses within our diverse collection. Until recently, we produced viral genome assemblies using only short-read sequencing technology. Here, we set out to determine if we could produce higher quality assemblies using long-read sequencing technology. To identify the optimal platform required for producing complete and accurate viral genome assemblies, we used a standardized workflow to extract nucleic acids from twenty-seven unique viruses from the Papillomaviridae, Polyomaviridae, Orthoherpesviridae, Adenoviridae, and Poxviridae families. We then sequenced the material on both the Oxford Nanopore Technologies® (ONT) and Illumina® platforms. Next, we produced individual de novo assemblies from the ONT® and Illumina® instruments as well as hybrid de novo assemblies using data from both platforms. All three assembly approaches were compared for completeness, depth, and accuracy to determine if one platform, the other, or both produced the optimal viral genome. Moving forward, ATCC will produce and publish genomes for the viruses maintained in our collection. Only the genomes that pass all quality control standards are published to the ATCC Genome Portal ( This platform allows users to interactively browse and search through indexed genomic data and metadata for a growing collection of over 4,000 ATCC microbial reference materials including viruses, bacteria, protists, and fungi. 

Download the poster to learn how we optimized our viral genome assemblies.



Corina Tabron, headshot

Corina Tabron, MS

Senior Biologist, ATCC

Corina first joined ATCC in 2021 as a biologist in the Sequencing and Bioinformatics Center where she routinely performed nucleic acid extractions on bacterial, fungal, and viral samples to be sequenced and published to the ATCC Genome Portal. She has since moved to become the department’s primary biologist for all Oxford Nanopore platforms. In her current role, she performs long-read sequencing for portal samples as well as researches new kits to advance ATCC's long-read applications. While joining ATCC, Corina attended George Mason University, where she earned an MS in Forensic Science.

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