VGEA

VGEA assembles and evaluates consensus RNA virus genomes from next-generation sequencing (NGS) data to characterize viral populations and their diversity.

Key Features:

• Workflow Integration: Built on the Snakemake workflow management system to integrate multiple bioinformatics tools into an automated pipeline.
• Human Contaminant Removal: Maps sequencing reads to the human genome using BWA to remove human-derived reads before viral analysis.
• Read Processing and Quality Control: Performs read trimming and quality control with fastp.
• De Novo Assembly: Conducts de novo assembly of forward and reverse reads with IVA to generate contigs.
• Read Pre-processing and Mapping: Uses shiver for read pre-processing and maps processed reads to a sample-tailored reference combining user-selected reference sequences and corrected contigs.
• Consensus Genome Reconstruction and Quasispecies Handling: Generates consensus genomes that account for high mutation rates and within-host quasispecies diversity.
• Assembly Evaluation: Assesses assembly quality using QUAST.
• Result Aggregation: Aggregates outputs and metrics from fastp, BWA, and QUAST using MultiQC.

Scientific Applications:

• Viral diversity and quasispecies analysis: Produces consensus genomes for characterization of within-host viral diversity and quasispecies.
• Epidemiology and transmission inference: Enables genome-based studies of viral epidemiology and transmission patterns.
• Evolutionary analyses: Provides assembled genomes suitable for viral evolution studies.
• Drug and vaccine research: Supplies high-quality genome assemblies to support drug and vaccine development research.

Methodology:

Snakemake orchestrates a workflow that maps reads to the human genome with BWA for contaminant removal, trims and performs QC with fastp, assembles contigs de novo with IVA, pre-processes and maps reads with shiver to a sample-tailored reference (user-selected references plus corrected contigs), evaluates assemblies with QUAST, and aggregates results with MultiQC.