Related Experiment Video
Updated: Jan 8, 2026
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 Mölder1,2, Johannes Köster1
1Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen, Essen 45131, Germany.
Summary:
We present Alignoth, a lightweight command line application that generates self-contained portable HTML reports of DNA sequencing read alignment pileups and additionally supports export to static formats such as PNG, SVG, and PDF as well as a JSON based embeddable representation. The HTML reports feature read name search and mapping-quality-based read highlighting, and require only minimal storage, making them practical to share, inspect, or integrate into broader reporting systems. They can be created in headless (i.e. terminal only) environments while being interactively inspected afterwards.
Availability And Implementation:
Alignoth is freely available under the MIT license at https://github.com/alignoth/alignoth (doi: https://doi.org/10.5281/zenodo.15837719). It is implemented in Rust and can be installed via Cargo or Conda.
