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Third-generation sequencing and the future of genomics

https://doi.org/10.1101/048603
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What this work says

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

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On Algorithmic Complexity of Biomolecular Sequence Assembly Problem
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Genomic mapping by fingerprinting random clones: A mathematical analysis
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The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development
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The impact of next-generation sequencing technology on genetics
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
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A comprehensive genetic map of the human genome based on 5,264 microsatellites
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The impact of next-generation sequencing technologies on HLA research
inferredcites →https://doi.org/10.1038/nature03895openalex-snapshot
The map-based sequence of the rice genome
inferredcites →https://doi.org/10.1038/nature08696openalex-snapshot
The sequence and de novo assembly of the giant panda genome
inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot
A map of human genome variation from population-scale sequencing
inferredcites →https://doi.org/10.1038/nature12028openalex-snapshot
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
inferredcites →https://doi.org/10.1038/nature12211openalex-snapshot
The Norway spruce genome sequence and conifer genome evolution
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/nature16996openalex-snapshot
Real-time, portable genome sequencing for Ebola surveillance
inferredcites →https://doi.org/10.1038/nbt.2280openalex-snapshot
Hybrid error correction and de novo assembly of single-molecule sequencing reads
inferredcites →https://doi.org/10.1038/nbt.2432openalex-snapshot
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/nbt.2478openalex-snapshot
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)
inferredcites →https://doi.org/10.1038/nbt.2705openalex-snapshot
A single-molecule long-read survey of the human transcriptome
inferredcites →https://doi.org/10.1038/nbt.2727openalex-snapshot
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions
inferredcites →https://doi.org/10.1038/nbt.2833openalex-snapshot
Whole-genome haplotyping using long reads and statistical methods
inferredcites →https://doi.org/10.1038/nbt.3200openalex-snapshot
De novo assembly of a haplotype-resolved human genome
inferredcites →https://doi.org/10.1038/nbt.3238openalex-snapshot
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
inferredcites →https://doi.org/10.1038/nbt.3432openalex-snapshot
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
inferredcites →https://doi.org/10.1038/nmeth.1858openalex-snapshot
Structural variation: the genome's hidden architecture
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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/nmeth.3454openalex-snapshot
Assembly and diploid architecture of an individual human genome via single-molecule technologies
inferredcites →https://doi.org/10.1038/nrg3054openalex-snapshot
Haplotype phasing: existing methods and new developments
inferredcites →https://doi.org/10.1073/pnas.1017351108openalex-snapshot
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/bts330openalex-snapshot
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
inferredcites →https://doi.org/10.1093/nar/gkt1113openalex-snapshot
ClinVar: public archive of relationships among sequence variation and human phenotype
inferredcites →https://doi.org/10.1101/gr.079053.108openalex-snapshot
De novo fragment assembly with short mate-paired reads: Does the read length matter?
inferredcites →https://doi.org/10.1101/gr.101360.109openalex-snapshot
Assembly of large genomes using second-generation sequencing
inferredcites →https://doi.org/10.1101/gr.193474.115openalex-snapshot
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
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.aae0344openalex-snapshot
Long-read sequence assembly of the gorilla genome
inferredcites →https://doi.org/10.1186/2047-217x-3-34openalex-snapshot
Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology
inferredcites →https://doi.org/10.1186/gb-2008-9-3-r55openalex-snapshot
Genome assembly forensics: finding the elusive mis-assembly
inferredcites →https://doi.org/10.1186/gb-2013-14-5-r51openalex-snapshot
Characterizing and measuring bias in sequence data
inferredcites →https://doi.org/10.1186/gb-2013-14-6-405openalex-snapshot
The advantages of SMRT sequencing
inferredcites →https://doi.org/10.1186/gb-2013-14-7-405openalex-snapshot
The advantages of SMRT sequencing
inferredcites →https://doi.org/10.1186/s13059-015-0587-3openalex-snapshot
Extending reference assembly models
inferredcites →https://doi.org/10.4137/bbi.s12462openalex-snapshot
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
inferredcites →https://doi.org/10.7554/elife.00569openalex-snapshot
The genome sequence of the colonial chordate, Botryllus schlosseri

What points at this work

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

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Adaptively Banded Smith-Waterman Algorithm for Long Reads and Its Hardware Accelerator
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Overlap Detection for a Genome Assembly Based on Genomic Signal Processing
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Minimap2 parallelization method based on distributed computing
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FPGA-Accelerated 3rd Generation DNA Sequencing
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Targeted enrichment of whole‐genome SNPs from highly burned skeletal remains
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The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance
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The genetics underlying natural variation of plant–plant interactions, a beloved but forgotten member of the family of biotic interactions
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WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
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Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
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A vast genomic deletion in the C56BL/6 genome affects different genes within the Ifi200 cluster on chromosome 1 and mediates obesity and insulin resistance
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Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature
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Identification of herbal medicine species of Lysimachia L. (Primulaceae) in Southern China using genome skimming
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Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data
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Ten steps to get started in Genome Assembly and Annotation
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The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies
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Complete Genome Sequence of Sphingobacterium sp. Strain CZ-2T Isolated from Tobacco Leaves Infected with Wildfire Disease
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Assessment of accuracy in identifying structural variants using third-generation sequencing for breast cancer in the absence of gold standard
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Filtering out redundant sites to alleviate the p>>n problem in genomic selection
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Recent Advances in the Ecoepidemiology, Virulence and Diagnosis of Cryptococcus neoformans and Cryptococcus gattii Species Complexes
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History of DNA Sequencing
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Metagenomic analysis of the vaginal microbiota in cows with ovarian cysts
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New generation genome sequencing methods
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Development of Polymer-Based In-Plane Nanopore for DNA Sequencing
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High-Performance Computing Frameworks for Large-Scale Genome Assembly
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Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics
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Long-Read Sequencing Emerging in Medical Genetics
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A Chromosome-Level Genome Assembly of Yellowtail Kingfish (Seriola lalandi)
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A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis
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Chromosome-level genome assembly of the Verasper variegatus provides insights into left eye migration
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Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach
inferred← citeshttps://doi.org/10.3389/fpls.2017.01317openalex-snapshot
Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses
inferred← citeshttps://doi.org/10.3389/fsufs.2021.624203openalex-snapshot
Plant Microbiota Beyond Farming Practices: A Review
inferred← citeshttps://doi.org/10.3390/ani14111578openalex-snapshot
Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals
inferred← citeshttps://doi.org/10.3390/forensicsci4040035openalex-snapshot
Sequencing Technologies in Forensic Microbiology: Current Trends and Advancements
inferred← citeshttps://doi.org/10.3390/genes10110846openalex-snapshot
The Value of Reference Genomes in the Conservation of Threatened Species
inferred← citeshttps://doi.org/10.3390/genes12060839openalex-snapshot
Nanopore Sequencing Unveils Diverse Transcript Variants of the Epithelial Cell-Specific Transcription Factor Elf-3 in Human Malignancies
inferred← citeshttps://doi.org/10.3390/genes17060633openalex-snapshot
CMSV: Long-Read-Based Structural Variation Detection Through a CNN–Mamba Model
inferred← citeshttps://doi.org/10.3390/genes7100088openalex-snapshot
RNA Interference in Moths: Mechanisms, Applications, and Progress
inferred← citeshttps://doi.org/10.3390/ijms26010372openalex-snapshot
Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics
inferred← citeshttps://doi.org/10.3390/jof7090743openalex-snapshot
Genomic Analyses of Penicillium Species Have Revealed Patulin and Citrinin Gene Clusters and Novel Loci Involved in Oxylipin Production
inferred← citeshttps://doi.org/10.3390/plants10071423openalex-snapshot
OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security
inferred← citeshttps://doi.org/10.3390/s17030588openalex-snapshot
DNA Sequencing Sensors: An Overview
inferred← citeshttps://doi.org/10.3390/s22062275openalex-snapshot
Basecalling Using Joint Raw and Event Nanopore Data Sequence-to-Sequence Processing
inferred← citeshttps://doi.org/10.3390/v13061020openalex-snapshot
Applications of Deep Mutational Scanning in Virology
inferred← citeshttps://doi.org/10.4103/jacm.jacm_15_22openalex-snapshot
Role of gene sequencing in the diagnosis, tracking and prevention of parasitic diseases – A brief review
inferred← citeshttps://doi.org/10.4137/bbi.s29333openalex-snapshot
Quality Assessment of Domesticated Animal Genome Assemblies
inferred← citeshttps://doi.org/10.48130/fra-0026-0008openalex-snapshot
Poplar genomics: a brief 20-year retrospective and future outlook
inferred← citeshttps://doi.org/10.5772/intechopen.112281openalex-snapshot
Research Advances and Perspectives of Conservation Genomics of Endangered Plants
inferred← citeshttps://doi.org/10.5897/ajb2018.16605openalex-snapshot
Next-generation sequencing platforms for latest livestock reference genome assemblies
inferred← citeshttps://doi.org/10.64898/2026.06.24.734161openalex-snapshot
A Draft Male Genome Assembly of the Slipper Lobster (Thenus australiensis) Reveals an XY System and a Validated Diagnostic Marker for Monosex Aquaculture
inferred← citeshttps://doi.org/10.70675/04070984z532az42cdz81e6z1a7b22173a48openalex-snapshot
Identification of the genetic bases of plant-plant cooperation in the model plant Arabidopsis thaliana
inferred← citeshttps://doi.org/10.70675/064ad1e7z430cz45c0zad30ze7e98249627copenalex-snapshot
Identification of genetic bases associated with natural variation of plant-plant interactions in arabidopsis thaliana
inferred← citeshttps://doi.org/10.70675/0f5289f1z1beaz4311z8029za15b04416483openalex-snapshot
Security of data stored into DNA molecules
inferred← citeshttps://doi.org/10.70675/0f7afe0bzb6b9z4993z9410z8cc46797da3eopenalex-snapshot
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inferred← citeshttps://doi.org/10.70675/7722069cz1034z4e64z8238z6126d6f7f792openalex-snapshot
DNA data storage algorithms and synchronization
inferred← citeshttps://doi.org/10.70675/82e19bd8z026ez4dabza0b6z3474c50172bcopenalex-snapshot
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inferred← citeshttps://doi.org/10.70675/8dac74eczafe9z4db6zbc3fz39c1be33d7dfopenalex-snapshot
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inferred← citeshttps://doi.org/10.70675/a5c24523zb66fz4178za69bz88cebf59b04copenalex-snapshot
Technologie µLAS pour l'analyse et la purification d'ADN de haut poids moléculaire
inferred← citeshttps://doi.org/10.7717/peerj.9564openalex-snapshot
Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
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