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Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

https://doi.org/10.1101/434118
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature08516openalex-snapshot
Origins and functional impact of copy number variation in the human genome
inferredcites →https://doi.org/10.1038/nature13907openalex-snapshot
Resolving the complexity of the human genome using single-molecule sequencing
inferredcites →https://doi.org/10.1038/nature15394openalex-snapshot
An integrated map of structural variation in 2,504 human genomes
inferredcites →https://doi.org/10.1038/nbt.3423openalex-snapshot
Three decades of nanopore sequencing
inferredcites →https://doi.org/10.1038/nbt.4060openalex-snapshot
Nanopore sequencing and assembly of a human genome with ultra-long reads
inferredcites →https://doi.org/10.1038/ncomms14061openalex-snapshot
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nrg1895openalex-snapshot
Primate segmental duplications: crucibles of evolution, diversity and disease
inferredcites →https://doi.org/10.1038/s41467-017-01343-4openalex-snapshot
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
inferredcites →https://doi.org/10.1038/s41467-018-08148-zopenalex-snapshot
Multi-platform discovery of haplotype-resolved structural variation in human genomes
inferredcites →https://doi.org/10.1038/s41592-018-0001-7openalex-snapshot
Accurate detection of complex structural variations using single-molecule sequencing
inferredcites →https://doi.org/10.1038/s41592-018-0002-6openalex-snapshot
Picky comprehensively detects high-resolution structural variants in nanopore long reads
inferredcites →https://doi.org/10.1038/s41598-017-07650-6openalex-snapshot
Rapid de novo assembly of the European eel genome from nanopore sequencing reads
inferredcites →https://doi.org/10.1086/374385openalex-snapshot
Genome Architecture Catalyzes Nonrecurrent Chromosomal Rearrangements
inferredcites →https://doi.org/10.1086/431652openalex-snapshot
Segmental Duplications and Copy-Number Variation in the Human Genome
inferredcites →https://doi.org/10.1093/bfgp/elv014openalex-snapshot
A decade of structural variants: description, history and methods to detect structural variation
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts480openalex-snapshot
Snakemake—a scalable bioinformatics workflow engine
inferredcites →https://doi.org/10.1093/bioinformatics/btv710openalex-snapshot
Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications
inferredcites →https://doi.org/10.1093/bioinformatics/btw742openalex-snapshot
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
inferredcites →https://doi.org/10.1093/bioinformatics/btx057openalex-snapshot
cyvcf2: fast, flexible variant analysis with Python
inferredcites →https://doi.org/10.1093/bioinformatics/btx699openalex-snapshot
Mosdepth: quick coverage calculation for genomes and exomes
inferredcites →https://doi.org/10.1093/bioinformatics/bty149openalex-snapshot
NanoPack: visualizing and processing long-read sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty841openalex-snapshot
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
inferredcites →https://doi.org/10.1093/nar/gkt958openalex-snapshot
The Database of Genomic Variants: a curated collection of structural variation in the human genome
inferredcites →https://doi.org/10.1101/193144openalex-snapshot
Multi-platform discovery of haplotype-resolved structural variation in human genomes
inferredcites →https://doi.org/10.1101/256719openalex-snapshot
A complete high quality nanopore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
inferredcites →https://doi.org/10.1101/267393openalex-snapshot
GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing
inferredcites →https://doi.org/10.1101/289579openalex-snapshot
A comprehensive toolkit to enable MinION sequencing in any laboratory
inferredcites →https://doi.org/10.1101/gr.113985.110openalex-snapshot
Adaptive seeds tame genomic sequence comparison
inferredcites →https://doi.org/10.1101/gr.214007.116openalex-snapshot
Discovery and genotyping of structural variation from long-read haploid genome sequence data
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot
LUMPY: a probabilistic framework for structural variant discovery
inferredcites →https://doi.org/10.1186/s12859-018-2252-9openalex-snapshot
npInv: accurate detection and genotyping of inversions using long read sub-alignment
inferredcites →https://doi.org/10.1186/s13059-015-0677-2openalex-snapshot
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
inferredcites →https://doi.org/10.1186/s13059-016-0973-5openalex-snapshot
Vcfanno: fast, flexible annotation of genetic variants
inferredcites →https://doi.org/10.1186/s13059-019-1856-3openalex-snapshot
NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION
inferredcites →https://doi.org/10.3389/fgene.2014.00381openalex-snapshot
Mappability and read length
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/jgm.3276openalex-snapshot
Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient with e14a3 BCR‐ABL1 transcript using Nanopore sequencing
inferred← citeshttps://doi.org/10.1007/978-1-0716-2237-7_10openalex-snapshot
A Practical Guide to Using Structural Variants for Genome-Wide Association Studies
inferred← citeshttps://doi.org/10.1007/s00401-019-01976-3openalex-snapshot
Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
inferred← citeshttps://doi.org/10.1016/j.biocel.2020.105799openalex-snapshot
Long-read sequencing to understand genome biology and cell function
inferred← citeshttps://doi.org/10.1016/j.tibtech.2019.02.003openalex-snapshot
Newest Methods for Detecting Structural Variations
inferred← citeshttps://doi.org/10.1038/s41588-021-00865-4openalex-snapshot
Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits
inferred← citeshttps://doi.org/10.1038/s41592-019-0669-3openalex-snapshot
Fast and accurate long-read assembly with wtdbg2
inferred← citeshttps://doi.org/10.1038/s41597-024-02929-6openalex-snapshot
A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii)
inferred← citeshttps://doi.org/10.1093/gigascience/giz075openalex-snapshot
Carbon-based archiving: current progress and future prospects of DNA-based data storage
inferred← citeshttps://doi.org/10.1093/nar/gkaa206openalex-snapshot
Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy
inferred← citeshttps://doi.org/10.1101/2021.10.28.466362openalex-snapshot
Genotyping of structural variation using PacBio high-fidelity sequencing
inferred← citeshttps://doi.org/10.1101/2025.06.29.662079openalex-snapshot
NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing
inferred← citeshttps://doi.org/10.1101/621862openalex-snapshot
Critical length in long read resequencing
inferred← citeshttps://doi.org/10.1111/tpj.17011openalex-snapshot
Structural variation discovery in wheat using PacBio high‐fidelity sequencing
inferred← citeshttps://doi.org/10.11606/d.3.2022.tde-05092022-084236openalex-snapshot
Accelerating the alignment phase of Minimap2 genome assembly algorithm Using GACT-X in a commercial Cloud FPGA machine.
inferred← citeshttps://doi.org/10.1186/s12915-022-01255-wopenalex-snapshot
Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology
inferred← citeshttps://doi.org/10.1186/s13059-019-1667-6openalex-snapshot
Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads
inferred← citeshttps://doi.org/10.1186/s13059-019-1856-3openalex-snapshot
NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION
inferred← citeshttps://doi.org/10.1186/s13059-019-1858-1openalex-snapshot
Evaluating nanopore sequencing data processing pipelines for structural variation identification
inferred← citeshttps://doi.org/10.1371/journal.pone.0254363openalex-snapshot
Evaluation of serverless computing for scalable execution of a joint variant calling workflow
inferred← citeshttps://doi.org/10.17760/d20416556openalex-snapshot
Optimized Levenshtein distance for clustering third-generation sequencing data
inferred← citeshttps://doi.org/10.18388/pb.2020_328openalex-snapshot
SEKWENCJONOWANIE NANOPOROWE I JEGO ZASTOSOWANIE W BIOLOGII
inferred← citeshttps://doi.org/10.31979/etd.n6cs-f4jwopenalex-snapshot
Comparison of an Oxford Nanopore Technologies Sequencing Platform to Existing Sequencing Methods for Differential Expression Studies
inferred← citeshttps://doi.org/10.33540/302openalex-snapshot
Novel computational approaches to predict and reconstruct bacterial plasmids
inferred← citeshttps://doi.org/10.33540/480openalex-snapshot
Leveraging technological opportunities in cancer genomics
inferred← citeshttps://doi.org/10.3389/fgene.2019.00426openalex-snapshot
Long-Read Sequencing Emerging in Medical Genetics
inferred← citeshttps://doi.org/10.4018/978-1-7998-1279-1.ch009openalex-snapshot
Human Knowledge and Expertise Platform for Managing Genomics Projects
inferred← citeshttps://doi.org/10.55003/cast.2023.06.23.009openalex-snapshot
Sequencing Approaches for Understanding the Pathogenic Features in Leptospira Genome
inferred← citeshttps://doi.org/10.6084/m9.figshare.19226894openalex-snapshot
Additional file 1 of Combined use of Oxford Nanopore and Illumina sequencing yields insights into soybean structural variation biology
inferred← citeshttps://doi.org/10.70675/21262276zb9afz4e12zbd5fz1fbd4577d093openalex-snapshot
Production of Hyper-Rec Genotypes in Brassicaceae crops
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