# Alignoth: portable and interactive visualization of read alignments

## TL;DR

Alignoth is a tool that creates portable and interactive visual reports of DNA sequencing read alignments for easy sharing and analysis.

## Contribution

Alignoth introduces a lightweight, portable, and interactive HTML-based visualization tool for read alignments.

## Key findings

- Alignoth generates self-contained HTML reports with features like read name search and mapping-quality highlighting.
- Reports can be exported to static formats like PNG, SVG, and PDF, and are suitable for headless environments.
- The tool is implemented in Rust and is available under the MIT license.

## Abstract

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.

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.