ArticlePloS one2013
Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 35 citations in OpenAlex.
- Cryo-EM structure of flagellotropic bacteriophage Chi.Structure (London, England : 1993) · 2024Article
- Complete genome sequences of Providencia bacteriophages PibeRecoleta, Stilesk and PatoteraRojo.BMC genomic data · 2023Article
- Isolation and Characterization of Chi-like Salmonella Bacteriophages Infecting Two Salmonella enterica Serovars, Typhimurium and EnteritidisPathogens (Basel, Switzerland) · 2022Article
- Whole Genome Sequencing and TnInternational journal of molecular sciences · 2020Article
- Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.Scientific reports · 2019Article
- Characterization of Flagellotropic, Chi-LikeViruses · 2019Article
- A Lytic Providencia rettgeri Virus of Potential Therapeutic Value Is a Deep-Branching Member of theApplied and environmental microbiology · 2017Article
- Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34.Scientific reports · 2017Article
- Genome Sequence ofGenome announcements · 2017Article
- Whole-Genome Analysis of Bartonella ancashensis, a Novel Pathogen Causing Verruga Peruana, Rural Ancash Region, Peru.Emerging infectious diseases · 2017Article
- SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.BMC bioinformatics · 2016Article
- Complete Genome Sequences of Three Important Methicillin-Resistant Clinical Isolates of Staphylococcus pseudintermedius.Genome announcements · 2016Article
- Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.BMC genomics · 2016Article
- Analysis of single nucleic acid molecules in micro- and nano-fluidics.Lab on a chip · 2016Review
- Complete Genome Sequence of Bartonella ancashensis Strain 20.00, Isolated from the Blood of a Patient with Verruga Peruana.Genome announcements · 2015Article
- Genetic variation and the de novo assembly of human genomes.Nature reviews. Genetics · 2015Review
- Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples.Journal of clinical and diagnostic research : JCDR · 2015Article
- Whole-Genome Sequence of "Candidatus Rickettsia asemboensis" Strain NMRCii, Isolated from Fleas of Western Kenya.Genome announcements · 2015Article
- Genome Sequence of Salmonella Phage χ.Genome announcements · 2015Article
- Whole genome mapping as a fast-track tool to assess genomic stability of sequenced Staphylococcus aureus strains.BMC research notes · 2014Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite major advances in next-generation sequencing, assembly of sequencing data, especially data from novel microorganisms or re-emerging pathogens, remains constrained by the lack of suitable reference sequences. De novo assembly is the best approach to achieve an accurate finished sequence, but multiple sequencing platforms or paired-end libraries are often required to achieve full genome coverage. In this study, we demonstrated a method to assemble complete bacterial genome sequences by integrating shotgun Roche 454 pyrosequencing with optical whole genome mapping (WGM). The whole genome restriction map (WGRM) was used as the reference to scaffold de novo assembled sequence contigs through a stepwise process. Large de novo contigs were placed in the correct order and orientation through alignment to the WGRM. De novo contigs that were not aligned to WGRM were merged into scaffolds using contig branching structure information. These extended scaffolds were then aligned to the WGRM to identify the overlaps to be eliminated and the gaps and mismatches to be resolved with unused contigs. The process was repeated until a sequence with full coverage and alignment with the whole genome map was achieved. Using this method we were able to achieved 100% WGRM coverage without a paired-end library. We assembled complete sequences for three distinct genetic components of a clinical isolate of Providencia stuartii: a bacterial chromosome, a novel bla NDM-1 plasmid, and a novel bacteriophage, without separately purifying them to homogeneity.
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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.