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aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly

RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, which is an obstacle for molecular biologists and researchers. Therefore, the higher...

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Autores principales: Surachat, Komwit, Taylor, Todd Duane, Wattanamatiphot, Wanicbut, Sukpisit, Sukgamon, Jeenkeawpiam, Kongpop
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404342/
https://www.ncbi.nlm.nih.gov/pubmed/36033257
http://dx.doi.org/10.1016/j.heliyon.2022.e10255
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author Surachat, Komwit
Taylor, Todd Duane
Wattanamatiphot, Wanicbut
Sukpisit, Sukgamon
Jeenkeawpiam, Kongpop
author_facet Surachat, Komwit
Taylor, Todd Duane
Wattanamatiphot, Wanicbut
Sukpisit, Sukgamon
Jeenkeawpiam, Kongpop
author_sort Surachat, Komwit
collection PubMed
description RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, which is an obstacle for molecular biologists and researchers. Therefore, the higher throughputs from NGS can only be accessed with the help of bioinformatics and computer science expertise. As the cost of sequencing is continuously falling, the use of RNA-seq seems certain to increase. To minimize the problems encountered by biologists and researchers in RNA-seq data analysis, we propose an automated platform with a web application that integrates various bioinformatics pipelines. The platform is intended to enable academic users to more easily analyze transcriptome datasets. Our automated Transcriptome Analysis Platform (aTAP) offers comprehensive bioinformatics workflows, including quality control of raw reads, trimming of low-quality reads, de novo transcriptome assembly, transcript expression quantification, differential expression analysis, and transcript annotation. aTAP has a user-friendly graphical interface, allowing researchers to interact with and visualize results in the web browser. This project offers an alternative way to analyze transcriptome data, by integrating efficient and well-known tools, that is simpler and more accessible to research communities. aTAP is freely available to academic users at https://atap.psu.ac.th/.
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spelling pubmed-94043422022-08-26 aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly Surachat, Komwit Taylor, Todd Duane Wattanamatiphot, Wanicbut Sukpisit, Sukgamon Jeenkeawpiam, Kongpop Heliyon Research Article RNA-seq is a sequencing technique that uses next-generation sequencing (NGS) to explore and study the entire transcriptome of a biological sample. NGS-based analyses are mostly performed via command-line interfaces, which is an obstacle for molecular biologists and researchers. Therefore, the higher throughputs from NGS can only be accessed with the help of bioinformatics and computer science expertise. As the cost of sequencing is continuously falling, the use of RNA-seq seems certain to increase. To minimize the problems encountered by biologists and researchers in RNA-seq data analysis, we propose an automated platform with a web application that integrates various bioinformatics pipelines. The platform is intended to enable academic users to more easily analyze transcriptome datasets. Our automated Transcriptome Analysis Platform (aTAP) offers comprehensive bioinformatics workflows, including quality control of raw reads, trimming of low-quality reads, de novo transcriptome assembly, transcript expression quantification, differential expression analysis, and transcript annotation. aTAP has a user-friendly graphical interface, allowing researchers to interact with and visualize results in the web browser. This project offers an alternative way to analyze transcriptome data, by integrating efficient and well-known tools, that is simpler and more accessible to research communities. aTAP is freely available to academic users at https://atap.psu.ac.th/. Elsevier 2022-08-15 /pmc/articles/PMC9404342/ /pubmed/36033257 http://dx.doi.org/10.1016/j.heliyon.2022.e10255 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Surachat, Komwit
Taylor, Todd Duane
Wattanamatiphot, Wanicbut
Sukpisit, Sukgamon
Jeenkeawpiam, Kongpop
aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title_full aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title_fullStr aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title_full_unstemmed aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title_short aTAP: automated transcriptome analysis platform for processing RNA-seq data by de novo assembly
title_sort atap: automated transcriptome analysis platform for processing rna-seq data by de novo assembly
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9404342/
https://www.ncbi.nlm.nih.gov/pubmed/36033257
http://dx.doi.org/10.1016/j.heliyon.2022.e10255
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