[HTML][HTML] Nanopore sequencing technology, bioinformatics and applications

Y Wang, Y Zhao, A Bollas, Y Wang, KF Au - Nature biotechnology, 2021 - nature.com
Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

[HTML][HTML] Nanopore sequencing and its application to the study of microbial communities

L Ciuffreda, H Rodríguez-Pérez, C Flores - Computational and structural …, 2021 - Elsevier
Since its introduction, nanopore sequencing has enhanced our ability to study complex
microbial samples through the possibility to sequence long reads in real time using …

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

A Payne, N Holmes, T Clarke, R Munro… - Nature …, 2021 - nature.com
Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool
by reversing the voltage across individual nanopores to reject specific sequences, enabling …

metaFlye: scalable long-read metagenome assembly using repeat graphs

M Kolmogorov, DM Bickhart, B Behsaz, A Gurevich… - Nature …, 2020 - nature.com
Long-read sequencing technologies have substantially improved the assemblies of many
isolate bacterial genomes as compared to fragmented short-read assemblies. However …

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen… - Nature …, 2021 - nature.com
High-throughput amplicon sequencing of large genomic regions remains challenging for
short-read technologies. Here, we report a high-throughput amplicon sequencing approach …

Beyond mass spectrometry, the next step in proteomics

W Timp, G Timp - Science Advances, 2020 - science.org
Proteins can be the root cause of a disease, and they can be used to cure it. The need to
identify these critical actors was recognized early (1951) by Sanger; the first biopolymer …

Benchmarking second and third-generation sequencing platforms for microbial metagenomics

V Meslier, B Quinquis, K Da Silva, F Plaza Oñate… - Scientific Data, 2022 - nature.com
Shotgun metagenomic sequencing is a common approach for studying the taxonomic
diversity and metabolic potential of complex microbial communities. Current methods …

Metagenomic tools in microbial ecology research

N Taş, AEE de Jong, Y Li, G Trubl, Y Xue… - Current Opinion in …, 2021 - Elsevier
Ability to directly sequence DNA from the environment permanently changed microbial
ecology. Here, we review the new insights to microbial life gleaned from the applications of …

Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing

YT Huang, PY Liu, PW Shih - Genome biology, 2021 - Springer
Nanopore sequencing has been widely used for the reconstruction of microbial genomes.
Owing to higher error rates, errors on the genome are corrected via neural networks trained …

The newest Oxford Nanopore R10. 4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling

T Zhang, H Li, S Ma, J Cao, H Liao… - Applied and …, 2023 - Am Soc Microbiol
The long-read amplicon provides a species-level solution for the community. With the
improvement of nanopore flowcells, the accuracy of Oxford Nanopore Technologies (ONT) …