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Detection and assembly of novel sequence insertions using Linked-Read technology

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What this work says

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

inferredcites →https://doi.org/10.1002/0471250953.bi1105s31openalex-snapshot

Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies

inferredcites →https://doi.org/10.1016/j.csbj.2017.10.002openalex-snapshot

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

inferredcites →https://doi.org/10.1016/j.gpb.2015.08.002openalex-snapshot

PacBio Sequencing and its Applications

inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot

A map of human genome variation from population-scale sequencing

inferredcites →https://doi.org/10.1038/nature09708openalex-snapshot

Mapping copy number variation by population-scale genome sequencing

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/nbt.2280openalex-snapshot

Hybrid error correction and de novo assembly of single-molecule sequencing reads

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.3432openalex-snapshot

Haplotyping germline and cancer genomes with high-throughput linked-read 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/nmeth.1527openalex-snapshot

Limitations of next-generation genome sequence assembly

inferredcites →https://doi.org/10.1038/nmeth.3737openalex-snapshot

TruSPAdes: barcode assembly of TruSeq synthetic long reads

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/nrg3117openalex-snapshot

Repetitive DNA and next-generation sequencing: computational challenges and solutions

inferredcites →https://doi.org/10.1038/nrg3933openalex-snapshot

Genetic variation and the de novo assembly of human genomes

inferredcites →https://doi.org/10.1038/s41467-018-05513-wopenalex-snapshot

De novo human genome assemblies reveal spectrum of alternative haplotypes in diverse populations

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/s41587-019-0074-6openalex-snapshot

An open resource for accurately benchmarking small variant and reference calls

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/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btq152openalex-snapshot

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btu545openalex-snapshot

MindTheGap: integrated detection and assembly of short and long insertions

inferredcites →https://doi.org/10.1093/bioinformatics/btv051openalex-snapshot

Methods for the detection and assembly of novel sequence in high-throughput sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btv273openalex-snapshot

PopIns: population-scale detection of novel sequence insertions

inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

inferredcites →https://doi.org/10.1093/bioinformatics/btx254openalex-snapshot

Discovery and genotyping of novel sequence insertions in many sequenced individuals

inferredcites →https://doi.org/10.1101/048603openalex-snapshot

Third-generation sequencing and the future of genomics

inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot

ABySS: A parallel assembler for short read sequence data

inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot

GENCODE: The reference human genome annotation for The ENCODE Project

inferredcites →https://doi.org/10.1101/gr.191189.115openalex-snapshot

Read clouds uncover variation in complex regions of the human genome

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.214874.116openalex-snapshot

Direct determination of diploid genome sequences

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/10.1101/gr.235499.118openalex-snapshot

Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics

inferredcites →https://doi.org/10.1186/s13073-017-0447-8openalex-snapshot

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases

inferredcites →https://doi.org/10.1371/journal.pone.0106689openalex-snapshot

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

inferredcites →https://doi.org/10.1534/genetics.115.180539openalex-snapshot

An Incomplete Understanding of Human Genetic Variation

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.07.018openalex-snapshot

Advances in optical mapping for genomic research

inferred← citeshttps://doi.org/10.1016/j.xgen.2023.100294openalex-snapshot

Genome graphs detect human polymorphisms in active epigenomic state during influenza infection

inferred← citeshttps://doi.org/10.1016/j.ygeno.2023.110568openalex-snapshot

Benchmarking of structural variant detection in the tetraploid potato genome using linked-read sequencing

inferred← citeshttps://doi.org/10.1038/s41576-019-0180-9openalex-snapshot

Structural variation in the sequencing era

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab359openalex-snapshot

Comparison of structural variants detected by optical mapping with long-read next-generation sequencing

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab749openalex-snapshot

Population-scale detection of non-reference sequence variants using colored de Bruijn graphs

inferred← citeshttps://doi.org/10.1101/2021.03.25.437002openalex-snapshot

LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads data

inferred← citeshttps://doi.org/10.1186/s12864-025-11398-zopenalex-snapshot

Large indel detection in region-based phased diploid assemblies from linked-reads

inferred← citeshttps://doi.org/10.1186/s13059-020-01975-8openalex-snapshot

VALOR2: characterization of large-scale structural variants using linked-reads

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/10.70675/8dcc42f6zaa6bz4ee2zb720z71c16f8f4885openalex-snapshot

Structural variant genotyping with long read data

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