Leveraging Long-Read and Short-Read Next-Generation Sequencing Data to Produce Reference Genomes for a Diverse Collection of Bacteriophages and their Hosts
ASM Microbe 2026
Washington, DC, United States
June 05, 2026Abstract
Bacteriophages have many different applications across many scientific disciplines spanning therapeutics to food sciences. Here, we demonstrate how we produced reference genomes for fifty bacteriophages as well as their hosts.
Bacteriophages were cultured following established growth conditions and then nucleic acids were extracted and whole-genome sequencing was completed following ISO 9001-compliant procedures. Sequencing was performed using both Illumina and Oxford Nanopore sequencing platforms, when nucleic acid yields were sufficient for long-read sequencing; samples with lower yields were processed using an Illumina-only workflow.
Once sequenced, genomes were assembled using SPAdes v4.0.0 with the Illumina short-read-only option or via a hybrid assembly approach utilizing either long-read-first, (Autocycler v0.5.2 or Flye v2.9.5-b1801), or a scaffold closing-approach with SPAdes v4.0.0. Together, this integrated sequencing and assembly workflow generated high-quality reference genomes, establishing a reproducible framework for bacteriophage genomics and downstream applications.
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Noah Wax, MS
Biologist, ATCC
Noah Wax is a Biologist in the Sequencing and Bioinformatics Center at ATCC. His work focuses on the extraction of nucleic acids from the various organisms and cell lines found within ATCC’s collection. Noah plays a vital role in supporting two significant initiatives: the ATCC Genome portal and ATCC Cell Line Land. The latter is an ongoing partnership between ATCC and QIAGEN aimed at providing authenticated reference RNA-seq data for all ATCC cell lines. Prior to joining ATCC, Noah received his master’s degree in biology from Virginia Tech where his work focused on utilizing comparative genomic approaches to study amphibian skin microbes.
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