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TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads

https://doi.org/10.1101/831248
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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-642-33122-0_25openalex-snapshot
FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation
inferredcites →https://doi.org/10.1016/j.ymeth.2012.05.001openalex-snapshot
Hi–C: A comprehensive technique to capture the conformation of genomes
inferredcites →https://doi.org/10.1023/a:1003716509180openalex-snapshot
DNA repeats in the human genome
inferredcites →https://doi.org/10.1038/nature11236openalex-snapshot
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells
inferredcites →https://doi.org/10.1038/nbt.1495openalex-snapshot
The potential and challenges of nanopore sequencing
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/ng.3119openalex-snapshot
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
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/s41587-019-0217-9openalex-snapshot
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
inferredcites →https://doi.org/10.1038/srep31900openalex-snapshot
DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies
inferredcites →https://doi.org/10.1073/pnas.1218696110openalex-snapshot
Whole-genome haplotyping by dilution, amplification, and sequencing
inferredcites →https://doi.org/10.1089/cmb.2015.0197openalex-snapshot
Gap Filling as Exact Path Length Problem
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
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/bioinformatics/btv465openalex-snapshot
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/hmg/ddq416openalex-snapshot
A window into third-generation sequencing
inferredcites →https://doi.org/10.1093/nar/gkh435openalex-snapshot
BLAST: at the core of a powerful and diverse set of sequence analysis tools
inferredcites →https://doi.org/10.1093/nar/gnh003openalex-snapshot
Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer
inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot
Direct determination of diploid genome sequences
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1101/gr.245126.118openalex-snapshot
Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
inferredcites →https://doi.org/10.1186/1471-2105-13-238openalex-snapshot
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
inferredcites →https://doi.org/10.1186/1471-2105-15-211openalex-snapshot
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
inferredcites →https://doi.org/10.1186/1471-2164-16-s3-s7openalex-snapshot
A pipeline for completing bacterial genomes using in silicoand wet lab approaches
inferredcites →https://doi.org/10.1186/1756-0500-7-371openalex-snapshot
FGAP: an automated gap closing tool
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/gb-2010-11-4-r41openalex-snapshot
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
inferredcites →https://doi.org/10.1186/gb-2012-13-6-r56openalex-snapshot
Toward almost closed genomes with GapFiller
inferredcites →https://doi.org/10.1186/s12859-021-04081-zopenalex-snapshot
SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme
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
inferredcites →https://doi.org/10.1186/s13742-016-0154-1openalex-snapshot
Draft genome of the living fossil Ginkgo biloba
inferredcites →https://doi.org/10.12688/f1000research.10571.2openalex-snapshot
Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis
inferredcites →https://doi.org/10.1371/journal.pone.0047768openalex-snapshot
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1371/journal.pone.0155327openalex-snapshot
GapBlaster—A Graphical Gap Filler for Prokaryote Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0216885openalex-snapshot
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
inferredcites →https://doi.org/10.5524/100613openalex-snapshot
Updated genome assembly of Ginkgo biloba
inferredcites →https://doi.org/10.6026/97320630009599openalex-snapshot
Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes

What points at this work

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

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Comparative Evolutionary Genomics in Insects
inferred← citeshttps://doi.org/10.1007/978-3-030-30347-1_12openalex-snapshot
Genomes of Other Species in Panax Linn
inferred← citeshttps://doi.org/10.1016/j.cell.2022.08.003openalex-snapshot
Design, construction, and in vivo augmentation of a complex gut microbiome
inferred← citeshttps://doi.org/10.1016/j.isci.2020.101662openalex-snapshot
African Arowana Genome Provides Insights on Ancient Teleost Evolution
inferred← citeshttps://doi.org/10.1016/j.isci.2021.103081openalex-snapshot
The genome of the naturally evolved obesity-prone Ossabaw miniature pig
inferred← citeshttps://doi.org/10.1038/s41597-025-04602-yopenalex-snapshot
A telomere-to-telomere genome assembly of the protandrous hermaphrodite blackhead seabream, Acanthopagrus schlegelii
inferred← citeshttps://doi.org/10.1038/s41597-025-05475-xopenalex-snapshot
A telomere-to-telomere gap-free genome assembly of the endangered humphead wrasse (Cheilinus undulatus)
inferred← citeshttps://doi.org/10.1093/bib/bbab033openalex-snapshot
A comprehensive review of scaffolding methods in genome assembly
inferred← citeshttps://doi.org/10.1093/gbe/evab029openalex-snapshot
A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida)
inferred← citeshttps://doi.org/10.1093/hr/uhad214openalex-snapshot
The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple ( Syzygium samarangense (Blume) Merr. and Perry)
inferred← citeshttps://doi.org/10.1101/2020.01.19.911958openalex-snapshot
Three genomes of Osteoglossidae shed light on ancient teleost evolution
inferred← citeshttps://doi.org/10.1101/2020.06.01.126995openalex-snapshot
Haplotype-Resolved Assembly for Synthetic Long Reads Using a Trio-Binning Strategy
inferred← citeshttps://doi.org/10.1101/2021.06.15.448618openalex-snapshot
Systematic dissection of a complex gut bacterial community
inferred← citeshttps://doi.org/10.1101/2024.11.25.625183openalex-snapshot
Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species
inferred← citeshttps://doi.org/10.1111/1755-0998.13207openalex-snapshot
De novo sequencing and chromosomal‐scale genome assembly of leopard coral grouper, Plectropomus leopardus
inferred← citeshttps://doi.org/10.1186/s12864-024-10232-2openalex-snapshot
Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis
inferred← citeshttps://doi.org/10.1186/s43897-023-00052-5openalex-snapshot
Telomere-to-telomere and haplotype-resolved genome of the kiwifruit Actinidia eriantha
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009254openalex-snapshot
Using de novo assembly to identify structural variation of eight complex immune system gene regions
inferred← citeshttps://doi.org/10.24072/pcjournal.140openalex-snapshot
Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants
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