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

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


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; Zenodo

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Profiling / methods
  • Nanopores*
  • Sequence Analysis, RNA / methods
  • Software*
  • Transcriptome