Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.
Sign Up to like & getrecommendations! Published in 2021 at "Nature methods"
DOI: 10.1038/s41592-021-01299-w
Abstract: Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonstrated a long read length, but… read more here.
Keywords: variant calling; haplotype aware; pepper margin; margin deepvariant ... See more keywords
Haplotype-aware graph indexes
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz575
Abstract: Abstract Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes. Results We augment… read more here.
Keywords: haplotype aware; https github; github com; haplotype ... See more keywords
Haplotype-aware sequence alignment to pangenome graphs
Sign Up to like & getrecommendations! Published in 2024 at "Genome Research"
DOI: 10.1101/2023.11.15.566493
Abstract: Modern pangenome graphs are built using haplotype-resolved genome assemblies. During read mapping to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes has been shown to improve genotyping accuracy. However, the existing… read more here.
Keywords: alignment; sequence; haplotype aware; pangenome ... See more keywords