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Applied Sciences
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Advances in Nanopore Sequencing Technology: Methodological Issues and Application
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Advances in Nanopore Sequencing Technology: Methodological Issues and Application

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Nanotechnology and Applied Nanosciences".

Deadline for manuscript submissions: closed (20 January 2022) | Viewed by 4591

Special Issue Editors

Dr. Cosimo Cumbo

E-Mail Website
Guest Editor
Hematology Section, Department of Emergency and Organ Transplantations, University of Bari “Aldo Moro”, 70124 Bari, Italy
Interests: hematological diseases; cancer genetics; molecular diagnostics; next generation sequencing; third generation sequencing; precision medicine
Special Issues, Collections and Topics in MDPI journals
Dr. Crescenzio Francesco Minervini

E-Mail Website
Guest Editor
Hematology section, Department of Emergency and Organ Transplantations, University of Bari “Aldo Moro”, 70124 Bari, Italy
Interests: molecular biology; genetics; cancer research; next generation sequencing; third generation sequencing

Special Issue Information

Dear Colleagues,

In recent years, third generation sequencing is transforming the standard way of conceiving genomic analyses. What was considered impossible only a few years ago in terms of throughput, potential, ease of use and costs, today is becoming achievable.

In 2012, the first long-read nanopore-based sequencer was released, overcoming the main limits of short-reads sequences generation and offering a revolutionizing approach finalized to have a profound, positive impact on society. In fact, nanopore sequencing (NS) applications span all areas of research: from metagenomics to plant disease, from human genomics to clinical research. NS allows an easier characterization of genomic regions that are difficult to be studied; it is the only approach able to perform the direct RNA sequencing and to detect the epigenetic base modifications without preliminary DNA or RNA treatment.

The present Special Issue aims to debate the most recent advances in NS technology, focusing on its methodological benefits and applications.  Contributions (research and review articles), addressing the NS performance in various “-omic” sciences: genomics, epigenomics and transcriptomics are welcome, with particular interest in NS aiming to allow the analysis of anything, by anyone, anywhere.

Dr. Cosimo Cumbo
Dr. Crescenzio Francesco Minervini
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • third generation sequencing
  • nanopore sequencing technology
  • MinION
  • lab-free analysis
  • direct RNA sequencing
  • direct epigenetic analysis
  • long-reads sequencing

Published Papers (2 papers)

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13 pages, 1072 KiB  
Article
Factors Affecting the Quality of Bacterial Genomes Assemblies by Canu after Nanopore Sequencing
by Antonella Schiavone, Nicola Pugliese, Rossella Samarelli, Cosimo Cumbo, Crescenzio Francesco Minervini, Francesco Albano and Antonio Camarda
Appl. Sci. 2022, 12(6), 3110; https://doi.org/10.3390/app12063110 - 18 Mar 2022
Cited by 2 | Viewed by 2359
Abstract
Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo [...] Read more.
Long-read sequencing (LRS), like Oxford Nanopore Technologies, is usually associated with higher error rates compared to previous generations. Factors affecting the assembly quality are the integrity of DNA, the flowcell efficiency, and, not least all, the raw data processing. Among LRS-intended de novo assemblers, Canu is highly flexible, with its dozens of adjustable parameters. Different Canu parameters were compared for assembling reads of Salmonellaenterica ser. Bovismorbificans (genome size of 4.8 Mbp) from three runs on MinION (N50 651, 805, and 5573). Two of them, with low quality and highly fragmented DNA, were not usable alone for assembly, while they were successfully assembled when combining the reads from all experiments. The best results were obtained by modifying Canu parameters related to the error correction, such as corErrorRate (exclusion of overlaps above a set error rate, set up at 0.40), corMhapSensitivity (the coarse sensitivity level, set to “high”), corMinCoverage (set to 0 to correct all reads, regardless the overlaps length), and corOutCoverage (corrects the longest reads up to the imposed coverage, set to 100). This setting produced two contigs corresponding to the complete sequences of the chromosome and a plasmid. The overall results highlight the importance of a tailored bioinformatic analysis. Full article
(This article belongs to the Special Issue Advances in Nanopore Sequencing Technology: Methodological Issues and Application)
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4 pages, 192 KiB  
Commentary
Third-Generation Sequencing in Clinical Practice: The New Era of Precision Medicine?
by Cosimo Cumbo, Crescenzio Francesco Minervini and Francesco Albano
Appl. Sci. 2022, 12(12), 6058; https://doi.org/10.3390/app12126058 - 15 Jun 2022
Viewed by 1348
Abstract
In the last decades, the spreading of next-generation sequencing (NGS) in clinical practice has considerably increased the genomic knowledge of several disorders. The recent advent of third-generation sequencing is transforming the standard way of conceiving clinical genomics, overcom-ing the main limits of conventional [...] Read more.
In the last decades, the spreading of next-generation sequencing (NGS) in clinical practice has considerably increased the genomic knowledge of several disorders. The recent advent of third-generation sequencing is transforming the standard way of conceiving clinical genomics, overcom-ing the main limits of conventional NGS technologies and achieving challenges so far considered unreasonable. What was impracticable only a few years ago, in terms of potential and affordability, now is becoming achievable. The new sequencing era will improve diagnostic and therapeutic ap-proaches, providing clinicians with valid support in their practice. Full article
(This article belongs to the Special Issue Advances in Nanopore Sequencing Technology: Methodological Issues and Application)
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