Alignoth : portable and interactive visualization of read alignments

This is the authors' abstract. We don't add key points for this paper.

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.