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A robust benchmark for germline structural variant detection

https://doi.org/10.1101/664623
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What this work says

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

inferredcites →https://doi.org/10.1016/j.ajhg.2018.07.011openalex-snapshot
Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia
inferredcites →https://doi.org/10.1016/j.cell.2018.12.019openalex-snapshot
Characterizing the Major Structural Variant Alleles of the Human Genome
inferredcites →https://doi.org/10.1016/j.jmoldx.2018.04.005openalex-snapshot
Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials
inferredcites →https://doi.org/10.1038/gim.2017.86openalex-snapshot
Long-read genome sequencing identifies causal structural variation in a Mendelian disease
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.2303openalex-snapshot
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
inferredcites →https://doi.org/10.1038/nbt.2835openalex-snapshot
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
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/nbt.4277openalex-snapshot
De novo assembly of haplotype-resolved genomes with trio binning
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/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/ng.3121openalex-snapshot
Comprehensive variation discovery in single human genomes
inferredcites →https://doi.org/10.1038/ng.3834openalex-snapshot
The impact of structural variation on human gene expression
inferredcites →https://doi.org/10.1038/ng.437openalex-snapshot
Personalized copy number and segmental duplication maps using next-generation sequencing
inferredcites →https://doi.org/10.1038/nmeth.3069openalex-snapshot
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/nmeth.4366openalex-snapshot
Genome-wide reconstruction of complex structural variants using read clouds
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/s41587-019-0054-xopenalex-snapshot
Best practices for benchmarking germline small-variant calls in human genomes
inferredcites →https://doi.org/10.1038/s41587-019-0074-6openalex-snapshot
An open resource for accurately benchmarking small variant and reference calls
inferredcites →https://doi.org/10.1038/s41587-019-0217-9openalex-snapshot
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
inferredcites →https://doi.org/10.1038/s41588-018-0316-4openalex-snapshot
Fast and accurate genomic analyses using genome graphs
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/sdata.2016.25openalex-snapshot
Extensive sequencing of seven human genomes to characterize benchmark reference materials
inferredcites →https://doi.org/10.1038/srep14493openalex-snapshot
Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods
inferredcites →https://doi.org/10.1073/pnas.1201904109openalex-snapshot
A public resource facilitating clinical use of genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btv204openalex-snapshot
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btv440openalex-snapshot
FermiKit: assembly-based variant calling for Illumina resequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btv478openalex-snapshot
svviz: a read viewer for validating structural variants
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/btw276openalex-snapshot
Read-based phasing of related individuals
inferredcites →https://doi.org/10.1093/bioinformatics/btw369openalex-snapshot
Assemblytics: a web analytics tool for the detection of variants from an assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btw753openalex-snapshot
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btz237openalex-snapshot
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing
inferredcites →https://doi.org/10.1093/gigascience/giy081openalex-snapshot
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution
inferredcites →https://doi.org/10.1101/085050openalex-snapshot
WhatsHap: fast and accurate read-based phasing
inferredcites →https://doi.org/10.1101/140699openalex-snapshot
Automated Structural Variant Verification in Human Genomes using Single-Molecule Electronic DNA Mapping
inferredcites →https://doi.org/10.1101/250647openalex-snapshot
TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
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/10.1101/gr.214767.116openalex-snapshot
HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot
Direct determination of diploid genome sequences
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1101/gr.221028.117openalex-snapshot
SvABA: genome-wide detection of structural variants and indels by local assembly
inferredcites →https://doi.org/10.1101/gr.222109.117openalex-snapshot
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
inferredcites →https://doi.org/10.1101/gr.231100.117openalex-snapshot
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
inferredcites →https://doi.org/10.1101/gr.234443.118openalex-snapshot
Resolving the full spectrum of human genome variation using Linked-Reads
inferredcites →https://doi.org/10.1126/science.1098918openalex-snapshot
Large-Scale Copy Number Polymorphism in the Human Genome
inferredcites →https://doi.org/10.1126/science.1138659openalex-snapshot
Strong Association of De Novo Copy Number Mutations with Autism
inferredcites →https://doi.org/10.1186/gb-2010-11-5-r52openalex-snapshot
Towards a comprehensive structural variation map of an individual human genome
inferredcites →https://doi.org/10.1186/s12864-015-1479-3openalex-snapshot
Assessing structural variation in a personal genome—towards a human reference diploid genome
inferredcites →https://doi.org/10.1186/s12864-016-2366-2openalex-snapshot
svclassify: a method to establish benchmark structural variant calls
inferredcites →https://doi.org/10.1186/s13059-018-1539-5openalex-snapshot
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
inferredcites →https://doi.org/10.1186/s13059-020-01975-8openalex-snapshot
VALOR2: characterization of large-scale structural variants using linked-reads
inferredcites →https://doi.org/10.1186/s13073-017-0479-0openalex-snapshot
Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis
inferredcites →https://doi.org/10.1371/journal.pcbi.1007933openalex-snapshot
A crowdsourced set of curated structural variants for the human genome
inferredcites →https://doi.org/10.1517/17425255.2016.1133586openalex-snapshot
Structural variants can be more informative for disease diagnostics, prognostics and translation than current SNP mapping and exon sequencing
inferredcites →https://doi.org/10.3389/fgene.2019.00426openalex-snapshot
Long-Read Sequencing Emerging in Medical Genetics
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing

What points at this work

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

inferred← citeshttps://doi.org/10.1002/humu.24466openalex-snapshot
Rapid genome sequencing for pediatrics
inferred← citeshttps://doi.org/10.1007/978-1-0716-2883-6_4openalex-snapshot
Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments
inferred← citeshttps://doi.org/10.1007/978-3-031-90252-9_37openalex-snapshot
ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly
inferred← citeshttps://doi.org/10.1016/j.ajhg.2021.06.001openalex-snapshot
Next-generation cytogenetics: Comprehensive assessment of 52 hematological malignancy genomes by optical genome mapping
inferred← citeshttps://doi.org/10.1016/j.csbj.2019.11.008openalex-snapshot
Challenges in identifying large germline structural variants for clinical use by long read sequencing
inferred← citeshttps://doi.org/10.1016/j.ymeth.2022.08.001openalex-snapshot
Automated filtering of genome-wide large deletions through an ensemble deep learning framework
inferred← citeshttps://doi.org/10.1038/s41467-019-13397-7openalex-snapshot
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data
inferred← citeshttps://doi.org/10.1038/s41467-020-18564-9openalex-snapshot
A diploid assembly-based benchmark for variants in the major histocompatibility complex
inferred← citeshttps://doi.org/10.1038/s41576-019-0180-9openalex-snapshot
Structural variation in the sequencing era
inferred← citeshttps://doi.org/10.1038/s41587-020-0503-6openalex-snapshot
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
inferred← citeshttps://doi.org/10.1038/s41587-020-0711-0openalex-snapshot
Chromosome-scale, haplotype-resolved assembly of human genomes
inferred← citeshttps://doi.org/10.1038/s41588-022-01043-wopenalex-snapshot
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
inferred← citeshttps://doi.org/10.1038/s41593-022-01031-7openalex-snapshot
Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain
inferred← citeshttps://doi.org/10.1080/09168451.2020.1786351openalex-snapshot
Identification of copy number variation and population analysis of the sacred lotus (Nelumbo nucifera)
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac058openalex-snapshot
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants
inferred← citeshttps://doi.org/10.1093/gigascience/giaa078openalex-snapshot
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
inferred← citeshttps://doi.org/10.1093/gigascience/giz110openalex-snapshot
Evaluation of computational genotyping of structural variation for clinical diagnoses
inferred← citeshttps://doi.org/10.1093/gigascience/giz141openalex-snapshot
Assessment of human diploid genome assembly with 10x Linked-Reads data
inferred← citeshttps://doi.org/10.1093/nargab/lqaa032openalex-snapshot
Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases
inferred← citeshttps://doi.org/10.1093/nargab/lqz018openalex-snapshot
De novo diploid genome assembly for genome-wide structural variant detection
inferred← citeshttps://doi.org/10.1101/2020.02.06.935742openalex-snapshot
Next generation cytogenetics: comprehensive assessment of 48 leukemia genomes by genome imaging
inferred← citeshttps://doi.org/10.1101/2020.04.13.039016openalex-snapshot
CNV-PG: a machine-learning framework for accurate copy number variation predicting and genotyping
inferred← citeshttps://doi.org/10.1101/2020.04.24.060202openalex-snapshot
Leveraging a WGS compression and indexing format with dynamic graph references to call structural variants
inferred← citeshttps://doi.org/10.1101/2020.05.22.111260openalex-snapshot
Learning What a Good Structural Variant Looks Like
inferred← citeshttps://doi.org/10.1101/2020.11.27.399857openalex-snapshot
Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite
inferred← citeshttps://doi.org/10.1101/2020.12.11.422022openalex-snapshot
An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development
inferred← citeshttps://doi.org/10.1101/2021.09.27.462057openalex-snapshot
An ensemble deep learning framework to refine large deletions in linked-reads
inferred← citeshttps://doi.org/10.1101/2022.02.12.480198openalex-snapshot
Improved structural variant discovery in hard-to-call regions using sample-specific string detection from accurate long reads
inferred← citeshttps://doi.org/10.1101/2023.09.11.557209openalex-snapshot
A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes
inferred← citeshttps://doi.org/10.1101/2025.09.29.679192openalex-snapshot
Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data
inferred← citeshttps://doi.org/10.1101/770396openalex-snapshot
Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective
inferred← citeshttps://doi.org/10.1101/810341openalex-snapshot
Accurate chromosome-scale haplotype-resolved assembly of human genomes
inferred← citeshttps://doi.org/10.1101/gr.263566.120openalex-snapshot
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
inferred← citeshttps://doi.org/10.1109/bibm52615.2021.9669571openalex-snapshot
An ensemble deep learning framework to refine large deletions in linked-reads
inferred← citeshttps://doi.org/10.1109/icbcb52223.2021.9459220openalex-snapshot
iPRIns: A Tool with the Improved Precision and Recall for Insertion Detection in the Human Genome
inferred← citeshttps://doi.org/10.1109/iccse51940.2021.9569325openalex-snapshot
IMDSVs: An integrated method based on machine learning and deep learning of calling structural variations from long-read data
inferred← citeshttps://doi.org/10.1126/science.abg8871openalex-snapshot
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
inferred← citeshttps://doi.org/10.1145/3582490openalex-snapshot
Theoretical Analysis of Edit Distance Algorithms
inferred← citeshttps://doi.org/10.1186/s12859-019-3145-2openalex-snapshot
MoMI-G: modular multi-scale integrated genome graph browser
inferred← citeshttps://doi.org/10.1186/s12859-020-03926-3openalex-snapshot
Set-theory based benchmarking of three different variant callers for targeted sequencing
inferred← citeshttps://doi.org/10.1186/s12864-020-07125-5openalex-snapshot
Towards a better understanding of the low recall of insertion variants with short-read based variant callers
inferred← citeshttps://doi.org/10.1186/s12864-022-08389-9openalex-snapshot
‘Nebbiolo’ genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.)
inferred← citeshttps://doi.org/10.1186/s13059-020-02047-7openalex-snapshot
Assembly and annotation of an Ashkenazi human reference genome
inferred← citeshttps://doi.org/10.1186/s13059-020-02107-yopenalex-snapshot
Long-read-based human genomic structural variation detection with cuteSV
inferred← citeshttps://doi.org/10.1186/s13059-020-1935-5openalex-snapshot
Opportunities and challenges in long-read sequencing data analysis
inferred← citeshttps://doi.org/10.1186/s13059-020-1941-7openalex-snapshot
Genotyping structural variants in pangenome graphs using the vg toolkit
inferred← citeshttps://doi.org/10.12688/f1000research.24887.1openalex-snapshot
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1007933openalex-snapshot
A crowdsourced set of curated structural variants for the human genome
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008397openalex-snapshot
Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009254openalex-snapshot
Using de novo assembly to identify structural variation of eight complex immune system gene regions
inferred← citeshttps://doi.org/10.21203/rs.3.rs-247574/v1openalex-snapshot
MaxDEL: Accurate and Efficient Calling Genomic Deletions From Single Molecular Real-Time Sequencing Using Integrated Method
inferred← citeshttps://doi.org/10.3389/fgene.2021.636239openalex-snapshot
stLFRsv: A Germline Structural Variant Analysis Pipeline Using Co-barcoded Reads
inferred← citeshttps://doi.org/10.3390/ijms20205013openalex-snapshot
Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective
inferred← citeshttps://doi.org/10.6084/m9.figshare.13544876openalex-snapshot
Additional file 1 of Set-theory based benchmarking of three different variant callers for targeted sequencing
inferred← citeshttps://doi.org/10.7287/peerj.12564v0.1/reviews/1openalex-snapshot
Peer Review #1 of "CNV-P: a machine-learning framework for predicting high confident copy number variations (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.12564v0.1/reviews/2openalex-snapshot
Peer Review #2 of "CNV-P: a machine-learning framework for predicting high confident copy number variations (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.12564v0.2/reviews/1openalex-snapshot
Peer Review #1 of "CNV-P: a machine-learning framework for predicting high confident copy number variations (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.12564v0.2/reviews/2openalex-snapshot
Peer Review #2 of "CNV-P: a machine-learning framework for predicting high confident copy number variations (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.12564v0.3/reviews/2openalex-snapshot
Peer Review #2 of "CNV-P: a machine-learning framework for predicting high confident copy number variations (v0.3)"
inferred← citeshttps://doi.org/10.7554/elife.67615openalex-snapshot
Local adaptation and archaic introgression shape global diversity at human structural variant loci
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