NanopoReaTA：一款用于纳米孔测序实时转录分析的用户友好型工具。

NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.

机构信息

Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany.

Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz 55128, Germany.

出版信息

Bioinformatics. 2023 Aug 1;39(8). doi: 10.1093/bioinformatics/btad492.

DOI:10.1093/bioinformatics/btad492

PMID:37549052

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10435370/

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.

摘要

牛津纳米孔技术（ONT）的测序平台为测序过程中的实时分析提供了极好的机会。该功能可以让我们尽早洞察实验数据，并加速潜在的决策过程，以便进一步分析，这在临床环境中可能特别重要。尽管已经存在一些用于实时分析 DNA 测序数据的工具，但目前还没有为具有有限生物信息学知识的科学家或医生设计的用于差异转录组数据分析的应用程序。在这里，我们介绍了 NanopoReaTA，这是一个用于 ONT 转录组 RNA 测序数据的用户友好型实时分析工具箱。正在运行或已完成的实验的测序结果通过基于 R Shiny 的图形用户界面进行处理，该界面集成了用于全转录组或基因特异性分析的 Nextflow 管道。NanopoReaTA 提供了正在进行的测序运行的可视化快照，从而实现了交互式测序和快速决策，也可以应用于临床案例。