NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Anna Wierczeiko
- Stefan Pastore
- Stefan Muendnich
- Anne M Busch
- Vincent Dietrich
- Mark Helm
- Tamer Butto
- Susanne Gerber
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:001057928100006&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/bioinformatics/btad492
- eISSN
- 1367-4811
- Externe Identifier
- Clarivate Analytics Document Solution ID: Q5LE7
- PubMed Identifier: 37549052
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- BIOINFORMATICS
- Artikelnummer
- ARTN btad492
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Titel
- NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
- Sub types
- Article
- Ausgabe der Zeitschrift
- 39
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Abstract
- <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>Oxford Nanopore Technologies’ (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge. Here, we introduce NanopoReaTA, a user-friendly real-time analysis toolbox for RNA-sequencing data from ONT. Sequencing results from a running or finished experiment are processed through an R Shiny-based graphical user interface with an integrated Nextflow pipeline for whole transcriptome or gene-specific analyses. NanopoReaTA provides visual snapshots of a sequencing run in progress, thus enabling interactive sequencing and rapid decision making that could also be applied to clinical cases.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>Github https://github.com/AnWiercze/NanopoReaTA; Zenodo https://doi.org/10.5281/zenodo.8099825.</jats:p> </jats:sec>
- Autoren
- Anna Wierczeiko
- Stefan Pastore
- Stefan Mündnich
- Anne M Busch
- Vincent Dietrich
- Mark Helm
- Tamer Butto
- Susanne Gerber
- DOI
- 10.1093/bioinformatics/btad492
- Editoren
- Anthony Mathelier
- eISSN
- 1367-4811
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- Bioinformatics
- Sprache
- en
- Online publication date
- 2023
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/bioinformatics/btad492
- Datum der Datenerfassung
- 2023
- Titel
- NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis
- Ausgabe der Zeitschrift
- 39
Datenquelle: Crossref
- Abstract
- <h4>Summary</h4>Oxford Nanopore Technologies' (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge. Here, we introduce NanopoReaTA, a user-friendly real-time analysis toolbox for RNA-sequencing data from ONT. Sequencing results from a running or finished experiment are processed through an R Shiny-based graphical user interface with an integrated Nextflow pipeline for whole transcriptome or gene-specific analyses. NanopoReaTA provides visual snapshots of a sequencing run in progress, thus enabling interactive sequencing and rapid decision making that could also be applied to clinical cases.<h4>Availability and implementation</h4>Github https://github.com/AnWiercze/NanopoReaTA; Zenodo https://doi.org/10.5281/zenodo.8099825.
- Addresses
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany.
- Autoren
- Anna Wierczeiko
- Stefan Pastore
- Stefan Mündnich
- Anne M Busch
- Vincent Dietrich
- Mark Helm
- Tamer Butto
- Susanne Gerber
- DOI
- 10.1093/bioinformatics/btad492
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Identifier: 37549052
- PubMed Central ID: PMC10435370
- Funding acknowledgements
- German Research Foundation:
- Landes Initiative Rheinland-Pfalz and the Resilience, Adaptation, and Longevity:
- Open access
- true
- ISSN
- 1367-4803
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- Bioinformatics (Oxford, England)
- Schlüsselwörter
- Gene Expression Profiling
- Sequence Analysis, RNA
- Software
- Nanopores
- Transcriptome
- Sprache
- eng
- Medium
- Open access status
- Open Access
- Paginierung
- btad492
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2023
- Titel
- NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.
- Sub types
- brief-report
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 39
Files
https://academic.oup.com/bioinformatics/article-pdf/39/8/btad492/51142598/btad492.pdf https://europepmc.org/articles/PMC10435370?pdf=render
Datenquelle: Europe PubMed Central
- Abstract
- SUMMARY: Oxford Nanopore Technologies' (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge. Here, we introduce NanopoReaTA, a user-friendly real-time analysis toolbox for RNA-sequencing data from ONT. Sequencing results from a running or finished experiment are processed through an R Shiny-based graphical user interface with an integrated Nextflow pipeline for whole transcriptome or gene-specific analyses. NanopoReaTA provides visual snapshots of a sequencing run in progress, thus enabling interactive sequencing and rapid decision making that could also be applied to clinical cases. AVAILABILITY AND IMPLEMENTATION: Github https://github.com/AnWiercze/NanopoReaTA; Zenodo https://doi.org/10.5281/zenodo.8099825.
- Date of acceptance
- 2023
- Autoren
- Anna Wierczeiko
- Stefan Pastore
- Stefan Mündnich
- Anne M Busch
- Vincent Dietrich
- Mark Helm
- Tamer Butto
- Susanne Gerber
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/37549052
- DOI
- 10.1093/bioinformatics/btad492
- eISSN
- 1367-4811
- Externe Identifier
- PubMed Central ID: PMC10435370
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- Bioinformatics
- Schlüsselwörter
- Software
- Nanopores
- Gene Expression Profiling
- Transcriptome
- Sequence Analysis, RNA
- Sprache
- eng
- Country
- England
- PII
- 7238212
- Datum der Veröffentlichung
- 2023
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2023
- Titel
- NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 39
Datenquelle: PubMed
- Beziehungen:
- Eigentum von