ArticleGenome biology2019
Paragraph: a graph-based structural variant genotyper for short-read sequence data.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
147 citing papers in PubMed.
- Genomic structural variations distinguishing archaic and modern humans are associated with neurodevelopment.iScience · 2026Article
- Genome-wide analysis of common structural variants in Alzheimer's disease identifies a risk-associated regulatory CCG repeat in FAM193B.Nature neuroscience · 2026Article
- Integrated pangenomics and population genomics reveal climate adaptation and maladaptation in an East Asian tree.Nature communications · 2026Article
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- A pangenome of tetraploid wheat reveals the genetic architecture underlying domestication and genomic diversity for breeding.Nature genetics · 2026Article
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Deciphering the Evolution Pattern of Structural Variations Overlapped With Repetitive Sequence During Cattle Evolution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome.Genome medicine · 2026Article
- Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.Genome biology · 2026Article
- Homologous recombination deficiency and hemizygosity drive resistance in breast cancer.Nature · 2026Article
- Structural Variation and 3D Genome-Driven DNA/RNA Methylation Divergence Contributing to Cotton Fiber Domestication.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Using the linear references from the pangenome to discover missing autism variants.Nature communications · 2026Article
- SVhet: towards accurate detection of germline heterozygous deletions using short reads.BMC bioinformatics · 2025Article
- PSVRP: a pig structural variant reference panel for complex trait genomics and precision breeding.BMC genomics · 2025Article
- Long-read structural variant discovery and targeted short read genotyping enables population scale characterization of structural variation in rhesus macaques.Genome biology · 2025Article
- Comprehensive detection of structural variations in long and short reads dataset of French cattle.Scientific reports · 2025Article
- A pangenome of maize provides genetic insights into drought resistance.Nature genetics · 2025Article
- Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.Genome biology and evolution · 2025Article
87 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long-read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry. Our analysis shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies.
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Registered trials
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.