ArticleGenome biology2021
NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Nanopore Sequencing for Chikungunya Virus: Principles and Application.Methods in molecular biology (Clifton, N.J.) · 2027Article
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- Amplicon-based long-read sequencing for accurate CYP2D6 gene deletion and duplication detection using CYP2D7 as a reference gene.The pharmacogenomics journal · 2026Article
- Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing.medRxiv : the preprint server for health sciences · 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
- Harnessing artificial intelligence in plant breeding: innovations in digital phenotyping and breeding methodologies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- SNooPy: a statistical framework for long-read metagenomic variant calling.Nucleic acids research · 2026Article
- Accelerated long-read variant calling with Clair3 for whole-genome sequencing.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Article
- A universal indel filtering workflow for both long-read and short-read NGS data.BMC research notes · 2026Article
- SnakeBITE: A SNAKEmake-Based Interface for Third-Generation Sequencing Data Analysis.Biomolecules · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- High-throughput characterization of 5886 HER2 variants identifies 112 new in cellulo gain-of-function mutations.Genomics · 2025Article
- Joint processing of long- and short-read sequencing data with deep learning improves variant calling.Cell reports methods · 2025Article
- Indel calling from ONT sequencing data of family trios via sparse attention and 3D convolution.Briefings in bioinformatics · 2025Article
- Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.International journal of molecular sciences · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- 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
1 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs using long-range haplotype information, then phases long reads with called SNPs and calls indels with local realignment. Evaluation on 8 human genomes demonstrates that NanoCaller generally achieves better performance than competing approaches. We experimentally validate 41 novel variants in a widely used benchmarking genome, which could not be reliably detected previously. In summary, NanoCaller facilitates the discovery of novel variants in complex genomic regions from long-read sequencing.
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