ArticleNature communications2021
Detecting and phasing minor single-nucleotide variants from long-read sequencing data.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- From fragments to full pictures: how long-read sequencing platforms are revolutionizing oncology research.Molecular biology reports · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- A new SNP comparison (SnpC) method for detecting unique/enriched gene-SNP variants and comparing population gene mutation diversity.BMC bioinformatics · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Long-read reconstruction of many diverse haplotypes with devider.Genome research · 2025Article
- Transcriptomic detection of Candidatus Allocryptoplasma (Anaplasmataceae) in Galápagos marine iguanas (Amblyrhynchus cristatus, Iguanidae).Parasites & vectors · 2025Article
- ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples.Nucleic acids research · 2025Article
- Genetic analysis using long-read sequencing to overcome the difficulties inResearch and practice in thrombosis and haemostasis · 2025Article
- Review
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- A High-Throughput Screening Strategy forMicroorganisms · 2025Article
- Learning From Full Characterization of HIV Proviruses in People Receiving Long-Acting Cabotegravir/Rilpivirine With a History of Replication on the Antiretroviral Classes.Open forum infectious diseases · 2025Article
- Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.Nature methods · 2024Article
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- Article
- Homozygous, Intragenic Tandem Duplication ofAmerican journal of respiratory cell and molecular biology · 2024Article
- Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution.Journal of molecular evolution · 2023Review
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, and co-infection of multiple pathogens. Detecting and phasing minor variants play an instrumental role in deciphering cellular genetic heterogeneity, but they are still difficult tasks because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, provide an opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrate that iGDA can accurately reconstruct haplotypes in closely related strains of the same species (divergence ≥0.011%) from long-read metagenomic data.
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