Journal
GENOME BIOLOGY
Volume 23, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02587-6
Keywords
Genome assembly; Haplotype; Virus; SARS-CoV-2; Long reads
Funding
- Chinese Scholarship Council
- Dutch Scientific Organization [639.072.309]
- European Union [956229, 872539]
- Projekt DEAL.
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Researchers have introduced a novel approach called Strainline that allows for the assembly of viral haplotypes from noisy long reads without a reference genome. Benchmarking on simulated and real datasets of varying complexity and diversity confirms the novelty and superiority of Strainline.
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.
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