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

作者：João Dourado Santos, Daniel Sobral, Miguel Pinheiro, Joana Isidro, Carlijn Bogaardt, Miguel Pinto, Rodrigo Eusébio, André Santos, Rafael Mamede, Daniel L. Horton, João Paulo Gomes, Laurent Bigarré, Jovita Fernández-Piñero, Ricardo Jorge Pais, Maurilia Marcacci, Ana Moreno, Tobias Lilja, Øivind Øines, Artur Rzeżutka, Élisabeth Mathijs, Steven Van Borm, Morten Rasmussen, Katja Spieß, Vítor Borges · 发表于：Genome Medicine · 年份：2024 · DOI：10.1186/s13073-024-01334-3 · 被引用次数：25 · 研究领域：Genomics and Phylogenetic Studies、SARS-CoV-2 and COVID-19 Research、Bacteriophages and microbial interactions

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, human and avian influenza, monkeypox, 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, coverin...