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

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37549052", "kind": "science-record", "revision": 4, "content_hash": "sha256:a5d2384d0928fd62af29441f08bfe0e3a03bf6279d4d720239c20f0100c6e34e", "created_at": "2026-11-01T19:02:19Z", "updated_at": "2026-11-01T22:52:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.", "doi": "10.1093/bioinformatics/btad492", "pmid": "37549052", "authors": ["Anna Wierczeiko", "Stefan Pastore", "Stefan Mündnich", "Anne M Busch", "Vincent Dietrich", "Mark Helm", "Tamer Butto", "Susanne Gerber"], "journal": "Bioinformatics (Oxford, England)", "year": 2023, "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.\nAVAILABILITY AND IMPLEMENTATION: Github https://github.com/AnWiercze/NanopoReaTA; Zenodo https://doi.org/10.5281/zenodo.8099825.", "claims": [{"id": "claim-method", "statement": "The subsequent downstream analyses are based on commonly used R packages such as DESeq2 (Love et al. 2014) for principal component analysis and differential expression analysis of gene and transcript expression, and DEXSeq (Anders et al. 2012) and DRIMSeq (Nowicka and Robinson 2016) for differential transcript usage (Fig. 1D and E).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37549052", "locator": "sections[6] \"2.4 Downstream analyses based on R\" paragraph 2", "quote": "The subsequent downstream analyses are based on commonly used R packages such as DESeq2 (Love et al. 2014) for principal component analysis and differential expression analysis of gene and transcript expression, and DEXSeq (Anders et al. 2012) and DRIMSeq (Nowicka and Robinson 2016) for differential transcript usage (Fig. 1D and E)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary data are available at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37549052", "locator": "sections[12] \"Supplementary data\" paragraph 2", "quote": "Supplementary data are available at Bioinformatics online."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37549052"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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