ArticleFrontiers in microbiology2017
A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.
Article in Frontiers in microbiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 38 citations in OpenAlex.
- Chromosome-level genome ofiScience · 2026Article
- Hybrid Whole-Genome Sequencing for Genetic Stability Assessment of Infectious Laryngotracheitis Virus Vaccine Strains.Vaccines · 2026Article
- The chromosome-level genome of Hemerocallis middendorffii provides new insights into the floral scents and color biosynthesis in Chinese native daylily.BMC plant biology · 2025Article
- Chromosome-level genome assembly of Phortica okadai, a vector of Thelazia callipaeda.Scientific data · 2024Article
- A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel StrainMicroorganisms · 2024Article
- Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing.BMC infectious diseases · 2023Article
- The role of plasmids in carbapenem resistant E. coli in Alameda County, California.BMC microbiology · 2023Article
- Chromosome-level assembly and analysis of the Thymus genome provide insights into glandular secretory trichome formation and monoterpenoid biosynthesis in thyme.Plant communications · 2022Article
- A combined de novo assembly approach increases the quality of prokaryotic draft genomes.Folia microbiologica · 2022Article
- Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance.Microbiology spectrum · 2022Article
- Article
- Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels.Frontiers in microbiology · 2022Review
- What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.Microorganisms · 2021Article
- TheMicroorganisms · 2020Article
- The genome evolution and low-phosphorus adaptation in white lupin.Nature communications · 2020Article
- Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat.Scientific reports · 2019Article
- Polyglutamine Repeats in Viruses.Molecular neurobiology · 2019Review
- Improved genome ofPeerJ · 2019Article
- Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.Nucleic acids research · 2018Article
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.
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.