VirION3

A hybrid long- and short-read workflow for viromics using Nanopore, PacBio, and Illumina data.

Overview

VirION3 is an integrated wet-lab-and-informatics pipeline combining long-read (Oxford Nanopore, PacBio) and short-read (Illumina) sequencing to improve the recovery, assembly, and ecological interpretation of viral genomes from environmental samples. It extends the earlier VirION and VirION2 methods.

Scientific or practical problem

Short-read-only viral metagenomics often fails to fully resolve genome structure, repeats, and microdiversity in viral populations. Long-read and hybrid approaches can recover more complete genomes, but need systematic benchmarking against established short-read methods before being adopted as standard practice.

My role

Developer, contributing to pipeline design, implementation, and benchmarking analysis comparing short-read and long-read/hybrid workflows.

Dataset or data type

Environmental viral metagenomes sequenced with Illumina, Oxford Nanopore, and PacBio platforms.

Methods and technologies

• Long-read assembly and hybrid (long+short read) assembly
• Pipeline benchmarking (genome recovery, accuracy, contiguity)
• Viral population analysis and microdiversity assessment
• Reproducible workflow implementation (Nextflow)

Workflow diagram

flowchart LR
  A[Illumina reads] --> D[Hybrid assembly]
  B[Nanopore reads] --> D
  C[PacBio reads] --> D
  D --> E[Viral genome recovery]
  E --> F[Population / microdiversity analysis]

Major results or outputs

Benchmarking comparisons quantifying differences in genome recovery, assembly accuracy, and bias between short-read-only and hybrid long+short-read approaches. (Full results pending publication.)

Challenges and decisions

Balancing the higher per-base error rate of long reads against their advantage in resolving repetitive and structurally complex viral genome regions — addressed through hybrid assembly strategies and careful benchmarking design.

Publications

Manuscript in preparation.

Code and documentation

Repository link pending public release.

Collaborators

Extends prior VirION/VirION2 methods developed within the Sullivan Lab, The Ohio State University.

Current status

Ongoing development and benchmarking.

Limitations or confidentiality note

This page describes methods and general goals only; specific results are withheld pending publication.