Nanopore sequencing technology, bioinformatics and applications

Nature Biotechnology, Journal Year: 2021, Volume and Issue: 39(11), P. 1348 - 1365

Published: Nov. 1, 2021

Language: Английский

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Long-read human genome sequencing and its applications

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(10), P. 597 - 614

Published: June 5, 2020

Language: Английский

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A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Journal Year: 2020, Volume and Issue: 12(5), P. 315 - 330

Published: May 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Language: Английский

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Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids

Nature Medicine, Journal Year: 2020, Volume and Issue: 27(1), P. 115 - 124

Published: Nov. 9, 2020

Language: Английский

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Co-infections: potentially lethal and unexplored in COVID-19

The Lancet Microbe, Journal Year: 2020, Volume and Issue: 1(1), P. e11 - e11

Published: April 24, 2020

Language: Английский

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Readfish enables targeted nanopore sequencing of gigabase-sized genomes

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(4), P. 442 - 450

Published: Nov. 30, 2020

Language: Английский

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mNGS in clinical microbiology laboratories: on the road to maturity

Critical Reviews in Microbiology, Journal Year: 2019, Volume and Issue: 45(5-6), P. 668 - 685

Published: Nov. 2, 2019

Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become topic of concern. We review the current implementation this new technology infectious disease diagnostics and discuss feasibility transforming mNGS into diagnostic test. Since 2008, numerous studies from over 20 countries have revealed practicality work-up undiagnosed diseases. performs well identifying rare, novel, difficult-to-detect coinfected pathogens directly samples presents great potential resistance prediction by antibiotic genes, providing evidence that used to guide treatment options improve stewardship. Many physicians recognized as last resort method address infection problems. Although several hurdles, such workflow validation, quality control, standardisation, data interpretation, remain before implemented routinely laboratories, they are temporary overcome rapidly evolving technologies. With more validated workflows, lower cost turnaround time, simplified interpretation criteria, will widely accepted practice. Overall, landscape microbiology ensure properly utilised diagnosis, both microbiologists should thorough understanding power limitations method.

Language: Английский

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Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(6)

Published: Feb. 1, 2021

Significance There is great interest in understanding how antibiotic resistance disseminated by MGEs (i.e., plasmids, insertion sequences, and integrons). We have systematically investigated their interactions mediating the horizontal transfer of combining silico genomic analysis a large collection complete bacterial plasmids (14,029) genomes (12,059), then confirmed we observe nature using direct experimental approaches. showed whole picture all IS-associated patterns AMR genes across different genetic backgrounds our results highlight significant relationships between conjugative ISs shaping dissemination genes.

Language: Английский

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Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing

Journal of Clinical Microbiology, Journal Year: 2019, Volume and Issue: 58(1)

Published: Oct. 17, 2019

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise use in the clinical laboratory. Challenges implementation so far include high cost, length of time to results, and need technical bioinformatics expertise. However, recent technological innovation nanopore from Oxford Nanopore Technologies (ONT) has potential address these challenges. ONT attractive platform laboratories adopt due its low rapid turnaround time, user-friendly pipelines. this method still faces problem base-calling accuracy compared other platforms. This review highlights general challenges pathogen detection specimens by metagenomic sequencing, advantages disadvantages platform, how research date supports future diagnostics.

Language: Английский

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Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS‐CoV‐2 and Other Respiratory Viruses

Small, Journal Year: 2020, Volume and Issue: 16(32)

Published: June 24, 2020

The ongoing global novel coronavirus pneumonia COVID-19 outbreak has engendered numerous cases of infection and death. diagnosis relies upon nucleic acid detection; however, currently recommended methods exhibit high false-negative rates are unable to identify other respiratory virus infections, thereby resulting in patient misdiagnosis impeding epidemic containment. Combining the advantages targeted amplification long-read, real-time nanopore sequencing, herein, sequencing (NTS) is developed detect SARS-CoV-2 viruses simultaneously within 6-10 h, with a limit detection ten standard plasmid copies per reaction. Compared its specificity for five common viruses, NTS reaches 100%. Parallel testing approved reverse transcription-polymerase chain reaction kits using 61 samples from suspected show that identifies more infected patients (22/61) as positive, while also effectively monitoring mutated sequences, categorizing types SARS-CoV-2, detecting test sample. thus suitable diagnosis; moreover, this platform can be further extended diagnosing pathogens.

Language: Английский

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