VGEA: an RNA viral assembly toolkit.

Area of Science:

• Bioinformatics
• Genomics
• Virology

Background:

• Next-generation sequencing (NGS) has expanded viral diversity studies.
• Viral genome analysis faces challenges from high mutation rates and quasispecies formation.
• Existing bioinformatics tools are often standalone and computationally intensive.

Purpose of the Study:

• To develop a flexible, user-friendly, all-in-one Snakemake workflow for RNA viral genome analysis.
• To integrate existing bioinformatics tools into a cohesive pipeline deployable on personal computers.
• To facilitate efficient viral genome assembly and quality assessment.

Main Methods:

• The VGEA workflow integrates tools such as fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, and MultiQC.
• It includes steps for human contaminant removal, read preprocessing, de novo assembly, reference-based mapping, and quality evaluation.
• The pipeline is designed for ease of use and can be deployed on a personal computer.

Main Results:

• VGEA was successfully tested and validated using SARS-CoV-2, HIV-1, and Lassa Virus datasets.
• The workflow provides a comprehensive solution for viral genome analysis from raw sequencing reads to quality-assessed assemblies.
• The pipeline effectively handles challenges like high mutation rates and quasispecies.

Conclusions:

• VGEA offers an accessible and efficient solution for analyzing RNA viral genomes.
• The workflow democratizes advanced viral genome analysis by enabling deployment on personal computers.
• VGEA is freely available on GitHub, promoting wider adoption and research in viral genomics.