Nanopore sequencing technology, bioinformatics and applications

Wang, Yunhao; Zhao, Yue; Bollas, Audrey; Wang, Yuru; Au, Kin Fai

doi:10.1038/s41587-021-01108-x

Cited by 929 publications

(682 citation statements)

References 390 publications

(435 reference statements)

Supporting

Mentioning

562

Contrasting

Unclassified

Order By: Relevance

“…Nonetheless, Nanopore reads usually have a relatively high error rate, limiting their reliability and usefulness. Overcoming these obstacles will require further breakthroughs in developing new nanopores, increasing throughput, optimizing base-calling methods, and bioinformatics pipelines [40]. Once these constraints are fixed, ONT will have a tremendous impact on the field of genomics.…”

Section: Discussionmentioning

confidence: 99%

Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus

Zhang

Wang

et al. 2021

Viruses

View full text Add to dashboard Cite

The TRS-mediated discontinuous transcription process is a hallmark of Arteriviruses. Precise assessment of the intricate subgenomic RNA (sg mRNA) populations is required to understand the kinetics of viral transcription. It is difficult to reconstruct and comprehensively quantify splicing events using short-read sequencing, making the identification of transcription-regulatory sequences (TRS) particularly problematic. Here, we applied long-read direct RNA sequencing to characterize the recombined RNA molecules produced in porcine alveolar macrophages during early passage infection of porcine reproductive and respiratory syndrome virus (PRRSV). Based on sequencing two PRRSV isolates, namely XM-2020 and GD, we revealed a high-resolution and diverse transcriptional landscape in PRRSV. The data revealed intriguing differences in subgenomic recombination types between the two PRRSVs while also demonstrating TRS-independent heterogeneous subpopulation not previously observed in Arteriviruses. We find that TRS usage is a regulated process and share the common preferred TRS in both strains. This study also identified a substantial number of TRS-mediated transcript variants, including alternative-sg mRNAs encoding the same annotated ORF, as well as putative sg mRNAs encoded nested internal ORFs, implying that the genetic information encoded in PRRSV may be more intensively expressed. Epigenetic modifications have emerged as an essential regulatory layer in gene expression. Here, we gained a deeper understanding of m5C modification in poly(A) RNA, elucidating a potential link between methylation and transcriptional regulation. Collectively, our findings provided meaningful insights for redefining the transcriptome complexity of PRRSV. This will assist in filling the research gaps and developing strategies for better control of the PRRS.

show abstract

Section: Discussionmentioning

confidence: 99%

Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus

Zhang

Wang

et al. 2021

Viruses

View full text Add to dashboard Cite

show abstract

“…Many ONT applications and tools exist (Wang et al, 2021 ), but specific tools for processing and consensus calling of amplicon sequences are limited. Several programs and pipelines are available to create a consensus sequence based on existing reference sequences (Krehenwinkel et al, 2019 ; Maloney et al, 2020 ; Moore et al, 2020 ; Sikolenko & Valentovich, 2021 ; Strassert et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences

Vierstraete

Braeckman

2022

Ecology and Evolution

View full text Add to dashboard Cite

Oxford Nanopore Technologies (ONT) is a third‐generation sequencing technology that is gaining popularity in ecological research for its portable and low‐cost sequencing possibilities. Although the technology excels at long‐read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high‐quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference‐free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.

show abstract

“…Recent advances in molecular biology technologies, such as nanopore sequencing, have enabled researchers to sequence and assemble very large genomes with high accuracy and throughput [1]. The landmark achievement is the release of the complete sequence of a human genome [2,3], with a total sequence length of around 3.1 gigabase pairs (Gb).…”

Section: Introductionmentioning

confidence: 99%

Fractal Analysis of DNA Sequences Using Frequency Chaos Game Representation and Small-Angle Scattering

Anitas

2022

IJMS

View full text Add to dashboard Cite

The fractal characteristics of DNA sequences are studied using the frequency chaos game representation (FCGR) and small-angle scattering (SAS) technique. The FCGR allows representation of the frequencies of occurrence of k-mers (oligonucleotides of length k) in the form of images. The numerically encoded data are then used in a SAS analysis to enhance hidden features in DNA sequences. It is shown that the simulated SAS intensity allows us to obtain the fractal dimensions and scaling factors at various scales. These structural parameters can be used to distinguish unambiguously between the scaling properties of complex hierarchical DNA sequences. The validity of this approach is illustrated on several sequences from: Escherichia coli, Mouse mitochondrion, Homo sapiens mitochondrion and Human cosmid.

show abstract

Nanopore sequencing technology, bioinformatics and applications

Cited by 929 publications

References 390 publications

Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus

Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus

Amplicon_sorter: A tool for reference‐free amplicon sorting based on sequence similarity and for building consensus sequences

Fractal Analysis of DNA Sequences Using Frequency Chaos Game Representation and Small-Angle Scattering

Contact Info

Product

Resources

About