ArticleScientific reports2016
GFinisher: a new strategy to refine and finish bacterial genome assemblies.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
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- Antimicrobial Potential of Marine Sponge-Associated Bacillus velezensis and Stutzerimonas stutzeri from the Indian Coast: A Genome Mining and Metabolite Profiling Approach.Current microbiology · 2025Article
- Biocontrol Potential of the New Codling Moth Granulovirus (CpGV) Strains.Microorganisms · 2024Article
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- Assembly and Genome Annotation of Different Strains of Apple Fruit Moth Virus (International journal of molecular sciences · 2024Article
- Therapeutics and prophylactic efficacy of novel lytic Escherichia phage vB_EcoS_PJ16 against multidrug-resistant avian pathogenic E. coli using in vivo study.International microbiology : the official journal of the Spanish Society for Microbiology · 2024Article
- Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes.Microbiology resource announcements · 2023Article
- Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain.BMC microbiology · 2023Article
- The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct.PLoS neglected tropical diseases · 2023Article
- Microaerobic degradation of crude oil and long chain alkanes by a new Rhodococcus strain from Gulf of Mexico.World journal of microbiology & biotechnology · 2023Article
- Analysis ofPeerJ · 2023Article
- Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate.Scientific reports · 2022Article
- A combined de novo assembly approach increases the quality of prokaryotic draft genomes.Folia microbiologica · 2022Article
- Genome Sequence of a Potent Biosurfactant-Producing Bacterium,Microbiology resource announcements · 2022Article
- Complete Genome Sequence ofMicrobiology resource announcements · 2022Article
- Draft Genome Sequence of Paenibacillus sonchi IIRRBNF1, a Nitrogen-Fixing and Plant Growth-Promoting Bacterium Isolated from Rice Rhizosphere.Microbiology resource announcements · 2022Article
- High Genomic Identity between Clinical and Environmental Strains ofAntibiotics (Basel, Switzerland) · 2021Article
- Characterization ofMicroorganisms · 2021Article
- Genomic analysis of Neisseria elongata isolate from a patient with infective endocarditis.FEBS open bio · 2021Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.
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