ArticleNature communications2019
Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 162 papers.
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Who cites it
162 citing papers in PubMed.
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- Protocol for haplotype-resolved structural variant detection via long-read sequencing using cuteHap.STAR protocols · 2026Article
- Phenotypic and genotypic analysis ofInfection and immunity · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking of real-time, field-deployable whole-genome sequencing ofMicrobial genomics · 2026Article
- DNA methylation profiles of quail blood cells by whole-genome bisulfite and Oxford Nanopore sequencing.Scientific data · 2026Article
- SNooPy: a statistical framework for long-read metagenomic variant calling.Nucleic acids research · 2026Article
- Candidate Genomic Features Associated with Persistence inMicroorganisms · 2026Article
- A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A repeat expansion in GOLGA8A is a major risk factor for atypical frontotemporal lobar degeneration with ubiquitin-positive inclusions.Nature genetics · 2026Article
- Recurrent Chromosome Destabilization Through Repeat-Mediated Rearrangements in a Fungal Pathogen.Genome biology and evolution · 2026Article
- Genome-sequencing of ocular fluid in a patient with syphilitic uveitis: Strain identification and antimicrobial resistance detection.American journal of ophthalmology case reports · 2026Article
- SnakeBITE: A SNAKEmake-Based Interface for Third-Generation Sequencing Data Analysis.Biomolecules · 2026Article
- Dynamic and Ongoing De Novo L1 Retrotransposition Contributes to Genome Plasticity and Intrapatient Heterogeneity in Ovarian Cancer.Cancer research · 2026Article
- Nanopore sequencing reveals hidden landscape of short L1 transductions in colorectal cancer.Communications biology · 2026Article
- NGSMHC: a simple bioinformatics tool for comprehensively typing major histocompatibility complex genes in non-human species using next-generation sequencing data.Animal bioscience · 2026Article
- A Global Assessment of the Transcription-Dependent Single Nucleotide Variants Relies on the Characteristics of RNA-Sequencing Technologies.Biomolecules · 2026Article
- Context-aware simulation enables systematic optimization of long-read mapping parameters.GigaScience · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
102 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome. Single-molecule sequencing (SMS) technologies such as Pacific Biosciences and Oxford Nanopore generate long reads that can potentially address the limitations of short-read sequencing. However, the high error rate of SMS reads makes it challenging to detect small-scale variants in diploid genomes. We introduce a variant calling method, Longshot, which leverages the haplotype information present in SMS reads to accurately detect and phase single-nucleotide variants (SNVs) in diploid genomes. We demonstrate that Longshot achieves very high accuracy for SNV detection using whole-genome Pacific Biosciences data, outperforms existing variant calling methods, and enables variant detection in duplicated regions of the genome that cannot be mapped using short reads.
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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.