Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection
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Summary
An initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections is demonstrated, and a novel, scalable pipeline for real-time analysis of MinION sequence data is demonstrated.
- Type
- preprint
- Published
- 2017-11-17
- Cited by
- 4
- References
- 30
- Access
- Open access
- OpenAlex
- https://openalex.org/W2770952292
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:90743441
Keywords
Minion, Nanopore sequencing, Metagenomics, Computational biology, DNA sequencing
References
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- Two-stage revision for prosthetic joint infection: predictors of outcome and the role of reimplantation microbiology
- Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
- Prospective Evaluation of Criteria for Microbiological Diagnosis of Prosthetic-Joint Infection at Revision Arthroplasty
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- Phenotypic and Genotypic Characterization of Arcanobacterium haemolyticum Isolates from Infections of Horses
- Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data
- Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing
- Centrifuge: rapid and sensitive classification of metagenomic sequences
- Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes
- Nextflow enables reproducible computational workflows
- Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing
- Singularity: Scientific containers for mobility of compute
- Polyamine transporter potABCD is required for virulence of encapsulated but not nonencapsulated Streptococcus pneumoniae
- Revision for prosthetic joint infection following hip arthroplasty
Cited by
- Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements
- Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer
- YAMP: a containerized workflow enabling reproducibility in metagenomics research
- Rapid Next-Generation Sequencing-Based Diagnostics of Bacteremia in Septic Patients.
- Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION TM nanopore sequencer
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