Haplotype-resolved de novo assembly of highly diverse virus genomes is critical in prevention, control and treatment of viral diseases. Current methods either can handle only relatively accurate short read data, or collapse haplotype-specific variations into consensus sequence. Here, we present Strainline, a novel approach to assemble viral haplotypes from noisy long reads without a reference genome. Strainline is the first approach to provide strain-resolved, full-length de novo assemblies of viral quasispecies from noisy third-generation sequencing data. Benchmarking on simulated and real datasets of varying complexity and diversity confirm this novelty and demonstrate the superiority of Strainline. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-021-02587-6).
【저자키워드】 SARS-CoV-2, virus, Haplotype, genome assembly, Long reads, 【초록키워드】 Treatment, Variation, dataset, Critical, Viral diseases, consensus sequence, Benchmarking, supplementary material, sequencing data, reference genome, de novo, full-length, virus genome, approach, current, viral quasispecy, 【제목키워드】 de novo, full-length,