BonoboFlow: Streamlined Viral Genome Assembly and Haplotype Reconstruction from Nanopore Reads

Viral genome analysis is crucial for understanding global virus diversity. Traditional methods are labor-intensive and unsuitable for large-scale studies, while next-generation sequencing faces challenges with genome fragmentation. Third-generation sequencing, like Oxford Nanopore (ONT), offers long reads but has high error rates. Our Nextflow pipeline, BonoboFlow, addresses these issues by standardizing error correction, genome assembly, and haplotype reconstruction, improving the accuracy and efficiency of viral genome analysis.