Towards population-scale long-read sequencing

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn

(2021) Ying Hu et al.   Nature Communications

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

(2021) Daniel Butler et al.   Nature Communications

Correction: Long-read trio sequencing of individuals with unsolved intellectual disability

(2021) Marc Pauper et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Optimized sample selection for cost-efficient long-read population sequencing

(2021) T. Rhyker Ranallo-Benavidez et al.   GENOME RESEARCH

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data

(2020) Xiao Chen et al.   GENETICS IN MEDICINE

Targeted nanopore sequencing with Cas9-guided adapter ligation

(2020) Timothy Gilpatrick et al.   NATURE BIOTECHNOLOGY

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

(2020) Wen-Biao Jiao et al.   Nature Communications

SVJedi: Genotyping structural variations with long reads

(2020) Lolita Lecompte et al.   BIOINFORMATICS

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

(2020) Dave Lutgen et al.   Molecular Ecology Resources

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

(2020) Matthew Halvorsen et al.   Nature Communications

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system

(2020) Will A. Overholt et al.   ENVIRONMENTAL MICROBIOLOGY

Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing

(2020) My Linh Thibodeau et al.   GENETICS IN MEDICINE

Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication

(2020) Yixuan Kou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Long‐read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

(2020) Harmeet Singh Chawla et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovery and population genomics of structural variation in a songbird genus

(2020) Matthias H. Weissensteiner et al.   Nature Communications

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

(2020) Satomi Mitsuhashi et al.   Genome Medicine

Regional sequence expansion or collapse in heterozygous genome assemblies

(2020) Kathryn C. Asalone et al.   PLoS Computational Biology

PhaseME: Automatic rapid assessment of phasing quality and phasing improvement

(2020) Sina Majidian et al.   GigaScience

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions

(2020) Paras Garg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data

(2020) Davide Bolognini et al.   GigaScience

Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy

(2020) Shubham Chandak et al.   BIOINFORMATICS

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

(2020) David Heller et al.   BIOINFORMATICS

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

(2020) Sam Kovaka et al.   NATURE BIOTECHNOLOGY

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

(2020) Alexander Payne et al.   NATURE BIOTECHNOLOGY

Chromosome-scale, haplotype-resolved assembly of human genomes

(2020) Shilpa Garg et al.   NATURE BIOTECHNOLOGY

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome

(2020) Dylan G. Maghini et al.   Nature Protocols

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

(2020) Ilia Minkin et al.   Nature Communications

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

(2020) Nazeefa Fatima et al.   Genes

SVIM: Structural Variant Identification using Mapped Long Reads

(2019) David Heller et al.   BIOINFORMATICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

(2019) Sarah Kingan et al.   Genes

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

(2019) Melissa Leija-Salazar et al.   Molecular Genetics & Genomic Medicine

Genome maps across 26 human populations reveal population-specific patterns of structural variation

(2019) Michal Levy-Sakin et al.   Nature Communications

Newest Methods for Detecting Structural Variations

(2019) Wouter De Coster et al.   TRENDS IN BIOTECHNOLOGY

Ancestral admixture is the main determinant of global biodiversity in fission yeast

(2019) Sergio Tusso et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

(2019) Carolin A. Müller et al.   NATURE METHODS

Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease

(2019) Jun Sone et al.   NATURE GENETICS

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

The presence and impact of reference bias on population genomic studies of prehistoric human populations

(2019) Torsten Günther et al.   PLoS Genetics

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Evaluation of computational genotyping of structural variation for clinical diagnoses

(2019) Varuna Chander et al.   GigaScience

Latest techniques to study DNA methylation

(2019) Quentin Gouil et al.   Essays in Biochemistry

Structural variation in the sequencing era

(2019) Steve S. Ho et al.   NATURE REVIEWS GENETICS

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

(2019) Hannes P. Eggertsson et al.   Nature Communications

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

(2019) Jethro S. Johnson et al.   Nature Communications

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

(2019) Volkan Sevim et al.   Scientific Data

Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data

(2019) Matteo Chiara et al.   BRIEFINGS IN BIOINFORMATICS

Assessing the performance of genome-wide association studies for predicting disease risk

(2019) Jonas Patron et al.   PLoS One

AnnotSV: an integrated tool for structural variations annotation

(2018) Véronique Geoffroy et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

(2018) Jonathan R Belyeu et al.   GigaScience

How complete are “complete” genome assemblies?-An avian perspective

(2018) Valentina Peona et al.   Molecular Ecology Resources

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

(2018) Michael Schmid et al.   NUCLEIC ACIDS RESEARCH

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

Long-read sequence and assembly of segmental duplications

(2018) Mitchell R. Vollger et al.   NATURE METHODS

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

(2018) Adam Ameur et al.   Genes

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Departure from Hardy Weinberg Equilibrium and Genotyping Error

(2017) Bowang Chen et al.   Frontiers in Genetics

High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system

(2017) Wirulda Pootakham et al.   Scientific Reports

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Human Structural Variation: Mechanisms of Chromosome Rearrangements

(2015) Brooke Weckselblatt et al.   TRENDS IN GENETICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

(2012) Eva-Maria Willing et al.   PLoS One

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH