ArticleBMC research notes2014
Employing whole genome mapping for optimal de novo assembly of bacterial genomes.
Article in BMC research notes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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.
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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
9 citing papers in PubMed.
- LMAS: evaluating metagenomic short de novo assembly methods through defined communities.GigaScience · 2022Article
- Article
- PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2017Review
- Gerbil: a fast and memory-efficientAlgorithms for molecular biology : AMB · 2017Article
- Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation.Antimicrobial agents and chemotherapy · 2015Article
- Misassembly detection using paired-end sequence reads and optical mapping data.Bioinformatics (Oxford, England) · 2015Article
- Whole genome mapping as a fast-track tool to assess genomic stability of sequenced Staphylococcus aureus strains.BMC research notes · 2014Article
- Computational methods for optical mapping.GigaScience · 2014Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDe novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies.
findingsUtilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies.
conclusionsWe demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
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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.