ArticleBMC bioinformatics2018
npInv: accurate detection and genotyping of inversions using long read sub-alignment.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India.BMC medical genomics · 2025Article
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A 69.9-kb long inverted repeat increases genome instability in a strain ofNAR genomics and bioinformatics · 2025Article
- Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast.Nature communications · 2024Article
- Mitochondrial GpC and CpG DNA Hypermethylation Cause Metabolic Stress-Induced Mitophagy and Cholestophagy.International journal of molecular sciences · 2023Article
- A Cas3-base editing tool for targetable in vivo mutagenesis.Nature communications · 2023Article
- Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species.Molecular biology and evolution · 2023Article
- Article
- Correction of a Factor VIII genomic inversion with designer-recombinases.Nature communications · 2022Article
- Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape.Genome biology · 2021Article
- Evaluation of Germline Structural Variant Calling Methods for Nanopore Sequencing Data.Frontiers in genetics · 2021Article
- Long-read-based human genomic structural variation detection with cuteSV.Genome biology · 2020Article
- Unpredicted central inversion in a sgRNA flanked by inverted repeats.Molecular biology reports · 2020Article
- Recurrent inversion toggling and great ape genome evolution.Nature genetics · 2020Article
- HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C.Bioinformatics (Oxford, England) · 2020Article
- Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR.Genome research · 2020Article
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
- Evolutionary and functional impact of common polymorphic inversions in the human genome.Nature communications · 2019Article
- Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome.Genome research · 2019Article
- Predicting Local Inversions Using Rectangle Clustering and Representative Rectangle Prediction.IEEE transactions on nanobioscience · 2019Article
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Authors and funding
6 authors.
Funding
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Abstract
backgroundDetection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored.
resultWe present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm the presence of two of these novel inversions. We show that there is a near linear relationship between the length of flanking IR and the minimum inversion size, without inverted repeats.
conclusionThe application of npInv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion.
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