Pod5Viewer: a GUI for inspecting raw nanopore sequencing data.

Vincent Dietrich, Nicolò Alagna, Mark Helm, Susanne Gerber, Tamer Butto

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Vincent DietrichInstitute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55128, Germany.

Nicolò AlagnaInstitute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55128, Germany.

Mark HelmInstitute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, 55128, Germany.ORCID 0000-0002-0154-0928

Susanne GerberInstitute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, 55128, Germany.ORCID 0000-0001-9513-0729

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

Funding

Landes Initiative Rheinland-Pfalz and the Resilience, Adaptation, and Longevity

6 · The paper itself

Abstract

motivationOxford Nanopore Technologies recently adopted the POD5 file format for storing raw nanopore sequencing data. The information stored in these files provides detailed insights into the sequencing features and enhances the understanding of raw nanopore data. However, the process of visualizing the data can be cumbersome, especially for users without programming skills. To address this issue, we developed the pod5Viewer, a GUI application for inspecting POD5 files.

resultsThe pod5Viewer offers straightforward access to raw sequencing data and associated metadata in POD5 files. It includes functionalities for viewing, plotting, and exporting individual reads. Designed with user-friendliness in mind, the pod5Viewer is easy to install and use, making it suitable for users with all technical backgrounds. AVAILABILITY AND IMPLEMENTATION: The pod5Viewer is available as open source from the pod5Viewer Github repository (https://github.com/dietvin/pod5Viewer).

Indexed as

Nanopore SequencingSoftwareNanoporesSequence Analysis, DNAUser-Computer Interface

Identifiers

PMID39657315

DOI10.1093/bioinformatics/btae665

PMCPMC11630908

What Socratic holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.