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Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost

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What this work says

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

inferredcites →https://doi.org/10.1007/s00439-014-1424-6openalex-snapshot

Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences

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/ng.3121openalex-snapshot

Comprehensive variation discovery in single human genomes

inferredcites →https://doi.org/10.1038/nmeth.3865openalex-snapshot

A hybrid approach for de novo human genome sequence assembly and phasing

inferredcites →https://doi.org/10.1073/pnas.0604040103openalex-snapshot

An algorithm for assembly of ordered restriction maps from single DNA molecules

inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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

QUAST: quality assessment tool for genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/jhered/esn077openalex-snapshot

Extremely Low Genetic Diversity in the Endangered Hawaiian Monk Seal (Monachus schauinslandi)

inferredcites →https://doi.org/10.1093/nar/gkl1044openalex-snapshot

Rapid DNA mapping by fluorescent single molecule detection

inferredcites →https://doi.org/10.1101/gr.086546.108openalex-snapshot

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot

Direct determination of diploid genome sequences

inferredcites →https://doi.org/10.1142/9789812702456_0037openalex-snapshot

FAST AND CHEAP GENOME WIDE HAPLOTYPE CONSTRUCTION VIA OPTICAL MAPPING

inferredcites →https://doi.org/10.1186/1471-2164-10-630openalex-snapshot

Identification of mammalian orthologs using local synteny

inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot

Versatile and open software for comparing large genomes

inferredcites →https://doi.org/10.1186/s12864-015-1871-zopenalex-snapshot

Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system

inferredcites →https://doi.org/10.1186/s12864-015-1911-8openalex-snapshot

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

What points at this work

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

inferred← citeshttps://doi.org/10.1002/ajmg.a.61540openalex-snapshot

New phenotypes associated with 3q29 duplication syndrome: Results from the 3q29 registry

inferred← citeshttps://doi.org/10.1007/978-1-4939-8724-5_13openalex-snapshot

From Short Reads to Chromosome-Scale Genome Assemblies

inferred← citeshttps://doi.org/10.1016/j.csbj.2017.10.002openalex-snapshot

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

inferred← citeshttps://doi.org/10.1016/j.isci.2020.101754openalex-snapshot

The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish

inferred← citeshttps://doi.org/10.1093/gigascience/giy124openalex-snapshot

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads

inferred← citeshttps://doi.org/10.1093/gigascience/giy168openalex-snapshot

New de novo assembly of the Atlantic bottlenose dolphin ( Tursiops truncatus ) improves genome completeness and provides haplotype phasing

inferred← citeshttps://doi.org/10.1101/195180openalex-snapshot

Entering the era of conservation genomics: Cost-effective assembly of the African wild dog genome using linked long reads

inferred← citeshttps://doi.org/10.1101/2022.03.31.486393openalex-snapshot

A chromosome-length assembly of the Hawaiian Monk seal ( Neomonarchus schauinslandi ) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”

inferred← citeshttps://doi.org/10.1101/2024.10.30.620815openalex-snapshot

Quantifying structural variants in chromosomes using landmark-based disparity

inferred← citeshttps://doi.org/10.1101/254250openalex-snapshot

Proteomics as a metrological tool to evaluate genome annotation accuracy following de novo genome assembly: a case study using the Atlantic bottlenose dolphin ( Tursiops truncatus )

inferred← citeshttps://doi.org/10.1101/696146openalex-snapshot

Recent evolutionary history of tigers highlights contrasting roles of genetic drift and selection

inferred← citeshttps://doi.org/10.1111/1755-0998.13443openalex-snapshot

Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

inferred← citeshttps://doi.org/10.1186/s12915-019-0734-5openalex-snapshot

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

inferred← citeshttps://doi.org/10.1186/s13059-019-1889-7openalex-snapshot

Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution

inferred← citeshttps://doi.org/10.1534/g3.118.200171openalex-snapshot

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

inferred← citeshttps://doi.org/10.1534/g3.118.200768openalex-snapshot

Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing

inferred← citeshttps://doi.org/10.3390/genes13020333openalex-snapshot

Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology

inferred← citeshttps://doi.org/10.3390/genes13071270openalex-snapshot

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability

inferred← citeshttps://doi.org/10.3390/genes14091696openalex-snapshot

Proteomics as a Metrological Tool to Evaluate Genome Annotation Accuracy Following De Novo Genome Assembly: A Case Study Using the Atlantic Bottlenose Dolphin (Tursiops truncatus)

inferred← citeshttps://doi.org/10.3390/ijms23020966openalex-snapshot

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

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