ArticlePloS one2018
Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Strain-Level Typing ofACS infectious diseases · 2025Article
- A trackable trinuclear platinum complex for breast cancer treatment.Nucleic acids research · 2025Article
- DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.PloS one · 2025Article
- Strain-level bacterial typing directly from patient samples using optical DNA mapping.Communications medicine · 2023Article
- Identification and characterization of plasmids carrying the mobile colistin resistance geneJAC-antimicrobial resistance · 2023Article
- A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids.Micromachines · 2021Article
- Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-ResistantAntibiotics (Basel, Switzerland) · 2021Article
- Identity ofMicroorganisms · 2021Article
- Combining dense and sparse labeling in optical DNA mapping.PloS one · 2021Article
- Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach.PloS one · 2021Article
- Cultivation-Free Typing of Bacteria Using Optical DNA Mapping.ACS infectious diseases · 2020Article
- Enzyme-free optical DNA mapping of the human genome using competitive binding.Nucleic acids research · 2019Article
- Article
- The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis.Microbial genomics · 2018Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard "foreign" contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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