ArticleGigaScience2020
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 340 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
340 citing papers in PubMed, 463 citations in OpenAlex.
- Haplotype-resolved genome of a dry-preservable cell line reveals chromosome evolution and DNA damage.Life science alliance · 2026Article
- Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco.Plant physiology · 2026Article
- Whole genome ofMicrobiology resource announcements · 2026Article
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Therapeutic potential of a novel virulent bacteriophage XQ-1 against avian pathogenic Escherichia coli infection in broiler chickens.Poultry science · 2026Article
- A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16.G3 (Bethesda, Md.) · 2026Article
- The telomere-to-telomere genome and comparative analysis from algae to higher plants reveal origin and evolution of biosynthesis of chlorogenic acid pathway and production in ramie (Horticulture research · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Chromosome-scale genome of European anchovy (Engraulis encrasicolus L., 1758) and comparative genomics uncover clupeid-specific immune gene expansions.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Two telomere-to-telomere Nelumbo genome assemblies reveal domestication history and empower precision breeding.Nature communications · 2026Article
- Mitogenome and Phylogeny of the Hairy Puffer Pao baileyi (Sontirat 1985).Biochemical genetics · 2026Article
- Rumen-derived Prevotella and Megasphaera elsdenii mitigate methane production through functional modulation of rumen microbial metabolism.Journal of animal science and biotechnology · 2026Article
- Draft genome sequence of hydrocarbon-utilizingMicrobiology resource announcements · 2026Article
- From screening to treatment:Microbiology spectrum · 2026Article
- A pseudochromosomal reference genome of the golden jackal, Canis aureus.The Journal of heredity · 2026Article
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- A telomere-to-telomere gapfree genome assembly of Triplophysa stoliczkae (Tibetan stone loach, family Nemacheilidae).Scientific data · 2026Article
- Gap-free telomere-to-telomere genome assembly of stone flounder (Kareius bicoloratus).Scientific data · 2026Article
- Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres.Genome biology · 2026Article
- The first telomere-to-telomere genome assembly of a freshwater bivalve: Gibbosula rochechouartii.Scientific data · 2026Article
280 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalyses that use genome assemblies are critically affected by the contiguity, completeness, and accuracy of those assemblies. In recent years single-molecule sequencing techniques generating long-read information have become available and enabled substantial improvement in contig length and genome completeness, especially for large genomes (>100 Mb), although bioinformatic tools for these applications are still limited.
findingsWe developed a software tool to close sequence gaps in genome assemblies, TGS-GapCloser, that uses low-depth (∼10×) long single-molecule reads. The algorithm extracts reads that bridge gap regions between 2 contigs within a scaffold, error corrects only the candidate reads, and assigns the best sequence data to each gap. As a demonstration, we used TGS-GapCloser to improve the scaftig NG50 value of 3 human genome assemblies by 24-fold on average with only ∼10× coverage of Oxford Nanopore or Pacific Biosciences reads, covering with sequence data up to 94.8% gaps with 97.7% positive predictive value. These improved assemblies achieve 99.998% (Q46) single-base accuracy with final inserted sequences having 99.97% (Q35) accuracy, despite the high raw error rate of single-molecule reads, enabling high-quality downstream analyses, including up to a 31-fold increase in the scaftig NGA50 and up to 13.1% more complete BUSCO genes. Additionally, we show that even in ultra-large genome assemblies, such as the ginkgo (∼12 Gb), TGS-GapCloser can cover 71.6% of gaps with sequence data.
conclusionsTGS-GapCloser can close gaps in large genome assemblies using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and completeness while maintaining high accuracy. The software is available at https://github.com/BGI-Qingdao/TGS-GapCloser.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.