New bioinformatics pipeline for the identification and detection of viral genomes from Oxford Nanopore sequencing

An example output plot generated by the pipeline

Pathogenic viruses and viroids infecting plants can result in significant economic and ecological losses. In recent years, advances in Oxford Nanopore Technologies (ONT) have enabled real-time sequencing of long sequences through portable sequencers and thus offered a new avenue for plant virus diagnostics and research. A team from Queensland University of Technology (QUT) led by Assoc Prof Roberto Barrero and the Queensland Cyber Infrastructure Foundation (QCIF), have developed a new bioinformatics pipeline that facilitates the detection of viruses and viroids from both amplicon and metagenomic ONT data using different analytical strategies.

The pipeline called ONTViSc (ONT-based viral screening) can: 1) perform a direct search on the sequenced reads, 2) generate clusters, 3) assemble the reads to generate longer contigs or 4) directly map reads to a known reference. The pipeline is written in Nextflow, ensuring that it is reproducible, scalable, and can be run on a diverse set of compute infrastructures. It was written by Dr Maely Gauthier and tested by Dr Magda Antczak. 

The workflow was developed in consultation with both researchers and diagnosticians at the Australian Government’s Department of Agriculture, Fisheries and Forestry (DAFF) to understand how it would best cater to their needs based on their current and projected internal usage of ONT, as they transition some of their processes to the new technology. The pipeline has been validated with edge samples and helped resolve the complete genome of novel plant viruses.

The ONTViSc pipeline is now available for anyone to deploy or adapt through QUT’s GitHub repository, and the how-to guide is available within the Australian BioCommons How-to Hub. 

Magda utilised the Australian Nextflow Seqera Service to develop, optimise and run the ONTViSc pipeline, and spoke about the benefits of this fully subsidised service in December at the Australian Bioinformatics and Computational Biology Society (ABACBS) National Seminar Series.

The completion of this pipeline development has led to an independent nation-wide project aimed at transforming biosecurity diagnostics by making standardised bioinformatics workflows and interactive reports accessible to all DAFF biosecurity sites. The project, DNA to Decisions: Concise communication of genomics data for easier decision making is supported by a partnership between Australian BioCommons (as part of Workflow Commons), QCIF, QUT and DAFF.