ArticleBioinformatics (Oxford, England)2024
Interactive visualization of nanopore sequencing signal data with Squigualiser.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 2026Article
- A Practical Comparison of Short- and Long-Read Metabarcoding Sequencing: Challenges and Solutions for Plastid Read Removal and Microbial Community Exploration of Seaweed Samples.Molecular ecology resources · 2025Article
- Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing.Cell reports methods · 2025Article
- A new compression strategy to reduce the size of nanopore sequencing data.Genome research · 2025Article
- A new compression strategy to reduce the size of nanopore sequencing data.Genome research · 2025Article
- Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.Nature methods · 2025Article
- Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis.Bioinformatics (Oxford, England) · 2025Article
- The enduring advantages of the SLOW5 file format for raw nanopore sequencing data.GigaScience · 2025Article
- Nanopore Current Events Magnifier (nanoCEM): a novel tool for visualizing current events at modification sites of nanopore sequencing.NAR genomics and bioinformatics · 2024Article
- Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.bioRxiv : the preprint server for biology · 2024Article
- Streamlining remote nanopore data access with slow5curl.GigaScience · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
motivationNanopore sequencing current signal data can be 'basecalled' into sequence information or analysed directly, with the capacity to identify diverse molecular features, such as DNA/RNA base modifications and secondary structures. However, raw signal data is large and complex, and there is a need for improved visualization strategies to facilitate signal analysis, exploration and tool development.
resultsSquigualiser (Squiggle visualiser) is a toolkit for intuitive, interactive visualization of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies instruments. Squigualiser is compatible with a wide range of alternative signal-alignment software packages and enables visualization of both signal-to-read and signal-to-reference aligned data at single-base resolution. Squigualiser generates an interactive signal browser view (HTML file), in which the user can navigate across a genome/transcriptome region and customize the display. Multiple independent reads are integrated into a 'signal pileup' format and different datasets can be displayed as parallel tracks. Although other methods exist, Squigualiser provides the community with a software package purpose-built for raw signal data visualization, incorporating a range of new and existing features into a unified platform. AVAILABILITY AND IMPLEMENTATION: Squigualiser is an open-source package under an MIT licence: https://github.com/hiruna72/squigualiser. The software was developed using Python 3.8 and can be installed with pip or bioconda or executed directly using prebuilt binaries provided with each release.
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What Socratic holds
Registered trials
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.