ArticleBioinformatics (Oxford, England)2024
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.American journal of human genetics · 2026Article
- Hunting for microsatellite instability in long-read data with Owl.PLoS computational biology · 2026Article
- nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.Bioinformatics (Oxford, England) · 2026Article
- Uniparental Disomy Reveals Hidden Genetic Causes of Congenital Heart Disease.Research square · 2026Article
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.Genome research · 2026Article
- Article
- A family portrait of the genomic factors shaping tandem repeat mutagenesis.bioRxiv : the preprint server for biology · 2026Article
- Integrative screening identifies functional variants and VNTRs underlying GWAS signals at the 5p15.33 multi-cancer susceptibility locus.medRxiv : the preprint server for health sciences · 2026Article
- Identification of de novo variants from parent-proband duos via long-read sequencing.American journal of human genetics · 2026Article
- Genome-wide classification of tumor-derived reads from bulk long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Article
- Transposable elements contribute substantially to naturally occurring genetic lethality in Drosophila melanogaster.PLoS biology · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Genome-wide methylation detection and episignature analysis using PacBio long-read sequencing.Genome medicine · 2026Article
- Pharmacokinetic recall study of Estonian Biobank participants with novel genetic variants in CYP2C19 and CYP2D6.NPJ genomic medicine · 2026Article
- Palindrome-mediated 16p13.3 triplications cause a recognizable neurodegenerative disorder with ataxia.American journal of human genetics · 2026Article
- Unravelling ring chromosome structures and formation mechanisms by short-read and long-read genomic sequencing.Genetics in medicine open · 2026Article
- Satellite DNA fragility accompanies complex genome rearrangements and ecDNA oncogene amplification in canine osteosarcomas.bioRxiv : the preprint server for biology · 2025Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationIn diploid organisms, phasing is the problem of assigning the alleles at heterozygous variants to one of two haplotypes. Reads from PacBio HiFi sequencing provide long, accurate observations that can be used as the basis for both calling and phasing variants. HiFi reads also excel at calling larger classes of variation, such as structural or tandem repeat variants. However, current phasing tools typically only phase small variants, leaving larger variants unphased.
resultsWe developed HiPhase, a tool that jointly phases SNVs, indels, structural, and tandem repeat variants. The main benefits of HiPhase are (i) dual mode allele assignment for detecting large variants, (ii) a novel application of the A*-algorithm to phasing, and (iii) logic allowing phase blocks to span breaks caused by alignment issues around reference gaps and homozygous deletions. In our assessment, HiPhase produced an average phase block NG50 of 480 kb with 929 switchflip errors and fully phased 93.8% of genes, improving over the current state of the art. Additionally, HiPhase jointly phases SNVs, indels, structural, and tandem repeat variants and includes innate multi-threading, statistics gathering, and concurrent phased alignment output generation. AVAILABILITY AND IMPLEMENTATION: HiPhase is available as source code and a pre-compiled Linux binary with a user guide at https://github.com/PacificBiosciences/HiPhase.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.