WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab076
Abstract: SUMMARY Many tools can reconstruct viral sequences based on next generation sequencing reads. Although existing tools effectively recover local regions, their accuracy suffers when reconstructing the whole viral genomes (strains). Moreover, they consume significant memory… read more here.
Keywords: whole genome; reconstructing whole; wglink reconstructing; viral haplotypes ... See more keywords
Reconstructing viral haplotypes using long reads
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac089
Abstract: MOTIVATION Most RNA viruses lack strict proofreading during replication. Coupled with a high replication rate, some RNA viruses can form a virus population containing a group of genetically-related but different haplotypes. Characterizing the haplotype composition… read more here.
Keywords: using long; haplotypes using; viral haplotypes; reconstructing viral ... See more keywords
A binning tool to reconstruct viral haplotypes from assembled contigs
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-3138-1
Abstract: BackgroundInfections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic… read more here.
Keywords: contig binning; viral haplotypes; binning tool; tool ... See more keywords