A comparison of structural variant calling from short-read and nanopore-based whole-genome sequencing using optical genome mapping as a benchmark

A comparison of structural variant calling from short-read and nanopore-based whole-genome sequencing using optical genome mapping as a benchmark

The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent–child trios, who had previously undergone short-read whole-genome...

Полное описание

Библиографические подробности
Главные авторы:	Pei, Y, Tanguy, M, Giess, A, Dixit, A, Wilson, LC, Gibbons, RJ, Twigg, SRF, Elgar, G, Wilkie, AOM
Формат:	Journal article
Язык:	English
Опубликовано:	MDPI 2024

Схожие документы

Whole Genome Assembly of Human Papillomavirus by Nanopore Long-Read Sequencing
по: Shuaibing Yang, и др.
Опубликовано: (2022-01-01)

Review of recurrently mutated genes in craniosynostosis supports expansion of diagnostic gene panels
по: Tooze, RS, и др.
Опубликовано: (2023)

Benchmarking Oxford Nanopore read alignment‐based insertion and deletion detection in crop plant genomes
по: Gözde Yildiz, и др.
Опубликовано: (2023-06-01)

Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing
по: Junhong Luo, и др.
Опубликовано: (2022-10-01)

Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing
по: Ying Ni, и др.
Опубликовано: (2023-01-01)

Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies
по: Binh Thanh Thai, и др.
Опубликовано: (2019-11-01)

Corrigendum: Systematic benchmarking of nanopore Q20+ kit in SARS-CoV-2 whole genome sequencing
по: Junhong Luo, и др.
Опубликовано: (2022-12-01)

Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates
по: Tu Luan, и др.
Опубликовано: (2024-07-01)

Comprehensive genetic analysis of facioscapulohumeral muscular dystrophy by Nanopore long-read whole-genome sequencing
по: Mingtao Huang, и др.
Опубликовано: (2024-05-01)

Evaluating the performance of a clinical genome sequencing program for diagnosis of rare genetic disease, seen through the lens of craniosynostosis
по: Hyder, Z, и др.
Опубликовано: (2021)

Long read sequencing characterises a novel structural variant, revealing underactive AKR1C1 with overactive AKR1C2 as a possible cause of severe chronic fatigue
по: Julia Oakley, и др.
Опубликовано: (2023-11-01)

Multiplex structural variant detection by whole-genome mapping and nanopore sequencing
по: Lahari Uppuluri, и др.
Опубликовано: (2022-04-01)

vcfdist: accurately benchmarking phased small variant calls in human genomes
по: Tim Dunn, и др.
Опубликовано: (2023-12-01)

Whole human genome 5’-mC methylation analysis using long read nanopore sequencing
по: Catarina Silva, и др.
Опубликовано: (2022-12-01)

Evaluating the performance of tools used to call minority variants from whole genome short-read data.
по: Said Mohammed, K, и др.
Опубликовано: (2018)

Improvement of large copy number variant detection by whole genome nanopore sequencing
по: Javier Cuenca-Guardiola, и др.
Опубликовано: (2023-08-01)

Craniosynostosis, inner ear, and renal anomalies in a child with complete loss of SPRY1 (sprouty homolog 1) function
по: Tooze, RS, и др.
Опубликовано: (2022)

Improved Whole Genome Sequence Resource of Phytophthora melonis CJ26, Using Long-Read Nanopore Sequencing
по: Shengdan Lu, и др.
Опубликовано: (2022-10-01)

Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness
по: Heather P. McLaughlin, и др.
Опубликовано: (2020-02-01)

A Distributed Whole Genome Sequencing Benchmark Study
по: Richard D. Corbett, и др.
Опубликовано: (2020-12-01)

Pan-genomic analysis of clonal bacterial samples using nanopore reads and genome graphs
по: Colquhoun, R
Опубликовано: (2019)

PB2386: ASSESSMENT OF NANOPORE LONG-READ WHOLE-GENOME SEQUENCING FOR THE DETECTION OF LARGE CHROMOSOMAL STRUCTURAL VARIANTS IN MANTLE CELL LYMPHOMA
по: Marcus Hansen, и др.
Опубликовано: (2023-08-01)

Benchmarking long-read genome sequence alignment tools for human genomics applications
по: Jonathan LoTempio, и др.
Опубликовано: (2023-12-01)

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 2 approved]
по: Ryan R. Wick, и др.
Опубликовано: (2019-12-01)

Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 4; peer review: 4 approved]
по: Ryan R. Wick, и др.
Опубликовано: (2021-02-01)

VANIR—NextFlow Pipeline for Viral Variant Calling and de Novo Assembly of Nanopore and Illumina Reads for High-Quality dsDNA Viral Genomes
по: Joan Martí-Carreras, и др.
Опубликовано: (2020-07-01)

Are we there yet? Benchmarking low-coverage nanopore long-read sequencing for the assembling of mitochondrial genomes using the vulnerable silky shark Carcharhinus falciformis
по: J. Antonio Baeza, и др.
Опубликовано: (2022-04-01)

Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand
по: Denis M. Nyaga, и др.
Опубликовано: (2024-11-01)

De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing
по: Sudhindra R. Gadagkar, и др.
Опубликовано: (2023-10-01)

Benchmarking Low-Frequency Variant Calling With Long-Read Data on Mitochondrial DNA
по: Theresa Lüth, и др.
Опубликовано: (2022-05-01)

Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
по: McNaughton, AL, и др.
Опубликовано: (2019)

Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
по: Anna L. McNaughton, и др.
Опубликовано: (2019-05-01)

Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies.
по: Nora Rieber, и др.
Опубликовано: (2013-01-01)

Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing
по: Zhao Chen, и др.
Опубликовано: (2020-09-01)

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads
по: Müller, C, и др.
Опубликовано: (2019)

Benchmarking phasing software with a whole-genome sequenced cattle pedigree
по: Claire Oget-Ebrad, и др.
Опубликовано: (2022-02-01)

Development of Erf-mediated craniosynostosis and pharmacological amelioration
по: Vogiatzi, A, и др.
Опубликовано: (2023)

Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data
по: Víctor García-Olivares, и др.
Опубликовано: (2023-01-01)

Benchmarking datasets for assembly-based variant calling using high-fidelity long reads
по: Hyunji Lee, и др.
Опубликовано: (2023-03-01)

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
по: Sergio Andreu-Sánchez, и др.
Опубликовано: (2021-05-01)