From Fragments to Full Circles: A Scalable Strategy for Complete Phage Genome Assembly

Poster

Gray six-legged bacteriophage flanked by two purple, floating rods.

Advances in Genome Biology and Technology (AGBT) 2026 General Meeting

Orlando, Florida, United States

February 25, 2026

Abstract

In this study, we introduce a targeted approach for improving phage genome assembly by leveraging high-quality, authenticated bacterial reference genomes available through the ATCC® Genome Portal (AGP). Sequenced reads from phage extractions were aligned to these curated reference genomes to perform precise in silico de-hosting, enabling the removal of host-derived bacterial sequences prior to assembly. Because short-read assemblies alone often result in fragmented or incomplete phage genomes, we supplemented this approach with Oxford Nanopore Technologies (ONT) long-read sequencing of phage-enriched material. The combined data were assembled using Autocycler, a pipeline optimized for circular genome detection and resolution.

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Presenter

Joseph Petrone, PhD

Senior Bioinformatician, Sequencing & Bioinformatics Center, ATCC

Joseph Petrone received his PhD from the University of Florida’s Department of Microbiology and Cell Sciences with a focus in bacterial genomics and metagenomic microbiome analysis. Joseph’s interest in curating authentic genomic databases and developing new bioinformatic software led him to join ATCC in 2023, where he now works as a bioinformatician for the Sequencing and Bioinformatics Center. His current focus is the continual development and curation of the ATCC Genome Portal. In his free time, you will find Joe either caring for his exotic plant collection or modifying and racing cars at the local dragstrip.

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