ArticleScientific reports2015
Completing bacterial genome assemblies: strategy and performance comparisons.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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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.
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.
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Who cites it
36 citing papers in PubMed.
- Full-length transcriptome characterization ofFrontiers in genetics · 2024Article
- Comparative genomics of clinicalMicrobiology (Reading, England) · 2023Article
- Full-length transcriptome ofFrontiers in genetics · 2023Article
- Draft Genome Sequence of Clostridium butyricum Strain 16-3, Isolated from Neonatal Feces.Microbiology resource announcements · 2022Article
- Construction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing.NAR genomics and bioinformatics · 2022Article
- Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow EndemicFrontiers in plant science · 2022Article
- Complete Genome Sequence of Lacticaseibacillus rhamnosus CAU 1365, Isolated from Kimchi.Microbiology resource announcements · 2021Article
- Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease.International journal of molecular sciences · 2021Review
- Streamlining data-intensive biology with workflow systems.GigaScience · 2021Article
- Article
- Complete Genome Sequence of Weissella cibaria Strain BM2, Isolated from Korean Kimchi.Microbiology resource announcements · 2020Article
- Complete Genome Sequence of Bacillus velezensis Strain DKU_NT_04, Isolated from a Traditional Korean Food Made from Soybeans (Cheonggukjang).Microbiology resource announcements · 2020Article
- Multiplexed Non-barcoded Long-Read Sequencing and Assembling Genomes of Bacillus Strains in Error-Free Simulations.Current microbiology · 2020Article
- Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance.Clinical pharmacology and therapeutics · 2019Review
- Sequencing-based methods and resources to study antimicrobial resistance.Nature reviews. Genetics · 2019Review
- Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.Briefings in bioinformatics · 2019Article
- TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data.G3 (Bethesda, Md.) · 2019Article
- Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding.Frontiers in microbiology · 2019Article
- Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.The Journal of antimicrobial chemotherapy · 2018Article
- Complete sequence of kenaf (Hibiscus cannabinus) mitochondrial genome and comparative analysis with the mitochondrial genomes of other plants.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Determining the genomic sequences of microorganisms is the basis and prerequisite for understanding their biology and functional characterization. While the advent of low-cost, extremely high-throughput second-generation sequencing technologies and the parallel development of assembly algorithms have generated rapid and cost-effective genome assemblies, such assemblies are often unfinished, fragmented draft genomes as a result of short read lengths and long repeats present in multiple copies. Third-generation, PacBio sequencing technologies circumvented this problem by greatly increasing read length. Hybrid approaches including ALLPATHS-LG, PacBio corrected reads pipeline, SPAdes, and SSPACE-LongRead, and non-hybrid approaches--hierarchical genome-assembly process (HGAP) and PacBio corrected reads pipeline via self-correction--have therefore been proposed to utilize the PacBio long reads that can span many thousands of bases to facilitate the assembly of complete microbial genomes. However, standardized procedures that aim at evaluating and comparing these approaches are currently insufficient. To address the issue, we herein provide a comprehensive comparison by collecting datasets for the comparative assessment on the above-mentioned five assemblers. In addition to offering explicit and beneficial recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly.
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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.