ArticleScientific reports2016
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.Scientific data · 2019Article
- Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome.Scientific reports · 2019Article
- Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life.Frontiers in microbiology · 2019Article
- Molecular tools for the pathologic diagnosis of central nervous system tumors.Neuro-oncology practice · 2019Review
- Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.PloS one · 2019Article
- Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer.Scientific reports · 2018Article
- From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy.Genome biology · 2018Review
- Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing.Scientific reports · 2018Article
- Genetic repertoires of anaerobic microbiomes driving generation of biogas.Biotechnology for biofuels · 2018Article
- De Novo Assembly of a NewThe Plant cell · 2017Article
- A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer.BMC infectious diseases · 2017Article
- Resolving plasmid structures inMicrobial genomics · 2017Article
- Comparative analysis of targeted long read sequencing approaches for characterization of a plant's immune receptor repertoire.BMC genomics · 2017Article
- BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation.Nucleic acids research · 2017Article
- Investigation of chimeric reads using the MinION.F1000Research · 2017Article
- A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.Frontiers in microbiology · 2017Article
- Article
- Approaches for in silico finishing of microbial genome sequences.Genetics and molecular biologyArticle
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores. While MinION long reads have an error rate substantially higher than the ones produced by short-read sequencing technologies, they can generate de novo assemblies of microbial genomes, after an initial correction step that includes alignment of Illumina sequencing data or detection of overlaps between Oxford Nanopore reads to improve accuracy. In this study, MinION reads were generated from the multi-chromosome genome of Agrobacterium tumefaciens strain LBA4404. Errors in the consensus two-directional (sense and antisense) "2D" sequences were first characterized by way of comparison with an internal reference assembly. Both Illumina-based correction and self-correction were performed and the resulting corrected reads assembled into high-quality hybrid and non-hybrid assemblies. Corrected read datasets and assemblies were subsequently compared. The results shown here indicate that both hybrid and non-hybrid methods can be used to assemble Oxford Nanopore reads into informative multi-chromosome assemblies, each with slightly different outcomes in terms of contiguity and accuracy.
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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.