INSaFLU-TELEVIR

INSaFLU-TELEVIR expands a bioinformatics platform for virus next-generation sequencing data analysis with a TELEVIR module for metagenomic virus identification and strengthened genomic surveillance workflows.

Key Features:

• Reference-based genome assembly for Oxford Nanopore technologies (ONT): A pipeline for consensus genome generation from ONT sequencing data.
• Automated SARS-CoV-2 lineage classification: Automated assignment of SARS-CoV-2 lineages from sequencing data.
• Nextclade analysis: Integration of Nextclade for viral sequence analysis and clade assignment.
• Nextstrain phylogeographic and temporal analysis: Phylogeographic and temporal analysis for SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), and a generic build for other viruses.
• algn2pheno mutation screening: Screening of mutations of interest using algn2pheno.
• TELEVIR metagenomic virus detection: Module for viral metagenomic detection with workflows combining viral enrichment or host depletion steps, classification software (Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus).
• findONTime real-time ONT detection: Tool for reducing costs and time between sample reception and diagnosis during ONT runs.
• INSaFLU snakemake version: A snakemake workflow version of INSaFLU pipelines for reference-based consensus generation.

Scientific Applications:

• Viral metagenomic detection: Detection of viruses in metagenomic samples through configurable workflows with multiple classification algorithms and databases.
• Routine genomic surveillance: Systematic monitoring of viral pathogens including SARS-CoV-2, influenza, monkeypox, and RSV through genome assembly, lineage classification, and phylogeographic analysis.
• Real-time virus detection during sequencing: Rapid identification of viruses during Oxford Nanopore sequencing runs to accelerate diagnostic turnaround.
• Mutation screening for phenotype prediction: Identification of mutations of interest to infer potential phenotypic characteristics.

Methodology:

Reference-based genome assembly pipelines for Illumina and Oxford Nanopore technologies; benchmarking against command line bioinformatics workflows; extensive benchmarking of state-of-the-art metagenomics software for TELEVIR module development.