ArticlePloS one2016
GapBlaster-A Graphical Gap Filler for Prokaryote Genomes.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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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.
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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.
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Who cites it
16 citing papers in PubMed.
- Advance in the assembly of the plant mitochondrial genomes using high-throughput DNA sequencing data of total cellular DNAs.Plant biotechnology journal · 2025Review
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- Biotechnological Key Genes of theMicroorganisms · 2023Article
- Genomic Insights into the Microbial AgentMicroorganisms · 2023Article
- Characterization of a NovelMicroorganisms · 2023Article
- Probiogenomics ofMicroorganisms · 2021Article
- TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads.GigaScience · 2020Article
- Article
- Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.Scientific reports · 2019Article
- LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly.GigaScience · 2019Article
- Genome sequencing and analysis ofPeerJ · 2019Article
- High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-ProducingGenome announcements · 2018Article
- Draft Genome Sequences ofGenome announcements · 2017Article
- Draft Genome Sequence ofGenome announcements · 2017Article
- Genomic analysis of four strains ofStandards in genomic sciences · 2017Article
- Approaches for in silico finishing of microbial genome sequences.Genetics and molecular biologyArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.
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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.