INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

Abstract

Background: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. Results: The routine genomic surveillance component was strengthened with new workflows and functionalities, including: i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; ii) automated SARS-CoV-2 lineage classification; iii) Nextclade analysis; iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, seasonal and avian influenza, mpox, respiratory syncytial virus (RSV A/B), as well as a “generic” build for other viruses); and, v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without Viral enrichment/Host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer) and databases (RefSeq viral genome, Virosaurus, etc), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. Conclusion: The accessibility, versatility and functionality of INSaFLU-TELEVIR is expected to supply public health laboratories and researchers with a user-oriented bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).