Work

Alignoth : portable and interactive visualization of read alignments

Year: 2025

Type: article

Abstract: 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btaf663

Authors: Felix Wiegand, Felix Mölder, Johannes Köster

Institutions: Essen University Hospital, University of Duisburg-Essen

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $3,989

Funder: Deutsche Forschungsgemeinschaft