Article
Biotechnology & Applied Microbiology
Alexander Belyayev, Ruslan Kalendar, Jirina Josefiova, Ladislava Pastova, Farzaneh Habibi, Vaclav Mahelka, Bohumil Mandak, Karol Krak
Summary: Two alternative models were proposed for the formation of derivative monomers from telomeric heptamer motifs of Arabidopsis-type. It was suggested that derivatization of TSs is a common process in plant genomes, but the occurrence and frequencies of derivatives may vary among genotypes. Additionally, the formation of non-canonical arrays of TSs, especially at chromosomal termini, may contribute to genomic variability in nature.
Review
Microbiology
Anzaan Dippenaar, Sander N. Goossens, Melanie Grobbelaar, Selien Oostvogels, Bart Cuypers, Kris Laukens, Conor J. Meehan, Robin M. Warren, Annelies van Rie
Summary: The application of portable next-generation sequencing devices is limited in the tuberculosis field, and more research investment is needed to unleash their full potential.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Laura Ciuffreda, Hector Rodriguez-Perez, Carlos Flores
Summary: The introduction of nanopore sequencing technology has significantly improved our ability to study complex microbial samples, allowing real-time sequencing of long reads with low cost and portability. This technology plays a crucial role in resolving complex genomic structures, accessing metagenome assembled genomes, and shows great potential in environmental microbial analysis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Microbiology
Laura A. Pavliscak, Jayaveeramuthu Nirmala, Vikash K. Singh, Kelly R. B. Sporer, Tasia M. Taxis, Pawan Kumar, Sagar M. Goyal, Sunil Kumar Mor, Declan C. Schroeder, Scott J. Wells, Casey J. Droscha
Summary: The study validated a near-complete genomic sequencing approach for the identification of BLV proviral genomes and characterized sequence identity or divergence in a dairy herd, indicating both vertical and horizontal transmission. Oxford Nanopore sequencing was supported for identifying viral SNPs for retrospective genetic contact tracing of BLV transmission.
Article
Chemistry, Multidisciplinary
Shanyu Zhang, Zhenyuan Cao, Pingping Fan, Yuqin Wang, Wendong Jia, Liying Wang, Kefan Wang, Yao Liu, Xiaoyu Du, Chengzhen Hu, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: Saccharides play critical roles in cellular activities, and the identification of their complex and similar structures presents a technical challenge. Researchers have developed a nanopore sensing strategy that can identify saccharides based on minor structural differences. They also trained a machine learning algorithm for automatic event classification and achieved a high accuracy score.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Review
Chemistry, Analytical
Bo Lin, Jianan Hui, Hongju Mao
Summary: Nanopore technology has become increasingly important in the field of life science and biomedical research, particularly in gene sequencing and biomolecular studies, showing promising applications in cancer diagnosis, virus detection, genome assembly, and other biomedical sensing fields.
Article
Plant Sciences
Joanne Mackie, Wycliff M. Kinoti, Sumit Chahal, David A. Lovelock, Paul R. Campbell, Lucy T. T. Tran-Nguyen, Brendan C. Rodoni, Fiona E. Constable
Summary: A targeted whole genome sequencing method has been developed for detecting cucumber green mottle mosaic virus, which can effectively address the challenges in genomic sequencing of plant viruses by enriching target nucleic acid and using Oxford Nanopore MinION sequencing technology. The results of the study show that this method can efficiently and accurately detect the virus, and also yield good results in degraded samples.
Article
Biotechnology & Applied Microbiology
Sophie A. Simon, Katharina Schmidt, Lea Griesdorn, Andre R. Soares, Till L. V. Bornemann, Alexander J. Probst
Summary: This study evaluated the use of lower-than-recommended DNA quantities for Nanopore library preparation and found that high-quality MAGs could still be recovered when the input level reached 35ng. Furthermore, Nanopore reads from input quantities as low as 1ng improved the quality of hybrid assemblies when combined with short-read data.
Review
Genetics & Heredity
Laura K. White, Jay R. Hesselberth
Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J. Debebe, Matthew Loose
Summary: Nanopore sequencers selectively sequence DNA molecules by reversing voltage, overcome computational limitations with GPU base-calling, enrich specific chromosomes and genes, and enable efficient screening of target gene panels without specialized sample preparation.
NATURE BIOTECHNOLOGY
(2021)
Article
Computer Science, Information Systems
Wenjie Hu, Yuxin Zhang, Hongrui Zhang, Weigang Chen
Summary: This paper proposes a hardware accelerator for accelerating the recognition of DNA sequencing barcodes using a barcode identification scheme combining cyclic shifting with dynamic programming. The experimental results demonstrate that the accelerator can achieve a speedup of two orders of magnitude for longer barcodes.
Article
Biochemical Research Methods
Dylan G. Maghini, Eli L. Moss, Summer E. Vance, Ami S. Bhatt
Summary: Utilizing a combination of short-read metagenomic sequencing and long-read sequencing, high-quality bacterial genomes can be obtained from the complex human gut microbiome, with some challenges to overcome.
Article
Biochemical Research Methods
Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim
Summary: VirPipe is a new pipeline for detecting viral genomes from Nanopore or Illumina sequencing, with streamlined installation and customization.
Article
Biochemical Research Methods
Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe Elie Gozlan, Marine Combe
Summary: This article introduces an amplicon-based nanopore sequencing pipeline for analyzing the genetic diversity of SARS-CoV-2 and other pathogens. The pipeline integrates multiple bioinformatics tools, allowing users with minimal bioinformatics skills to perform downstream analysis steps with a simple command line and configuration file.
