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Updated: Jan 8, 2026

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Alignoth: portable and interactive visualization of read alignments.

Felix Wiegand¹, Felix Mölder^1,2, Johannes Köster¹

¹Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, Essen 45131, Germany.

Bioinformatics (Oxford, England)

|December 14, 2025

Summary

This summary is machine-generated.

Alignoth is a new command-line tool that creates portable HTML reports for DNA sequencing alignment pileups. These reports are lightweight, searchable, and exportable to various static formats for easy sharing and integration.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

DNA sequencing generates large datasets requiring efficient analysis.
Visualizing read alignment pileups is crucial for genomic data interpretation.
Existing tools may lack portability or interactive features for alignment visualization.

Purpose of the Study:

To introduce Alignoth, a novel command-line application for generating DNA sequencing alignment reports.
To provide a lightweight and portable solution for visualizing read alignment pileups.
To enhance the sharing and integration of genomic analysis results.

Main Methods:

Developed Alignoth as a command-line application using the Rust programming language.
Implemented features for generating self-contained, portable HTML reports.
Enabled export functionality to static formats (PNG, SVG, PDF) and JSON.

Main Results:

Alignoth produces HTML reports with interactive features like read name search and mapping-quality highlighting.
Reports are minimal in storage requirements, facilitating practical sharing.
The application supports headless environment generation with post-hoc interactive inspection.

Conclusions:

Alignoth offers a practical and efficient method for reporting DNA sequencing alignment pileups.
Its portability and export options make it valuable for diverse reporting workflows.
The tool enhances accessibility and usability of genomic alignment data visualization.