{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T20:16:10Z","timestamp":1767816970356,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,15]],"date-time":"2025-12-15T00:00:00Z","timestamp":1765756800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"DFG Research Training Group 2535 Knowledge"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf663","type":"journal-article","created":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T13:01:55Z","timestamp":1765544515000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>Alignoth<\/i>\n                    : portable and interactive visualization of read alignments"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-0725-2120","authenticated-orcid":false,"given":"Felix","family":"Wiegand","sequence":"first","affiliation":[{"name":"Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen , Essen 45131,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3976-9701","authenticated-orcid":false,"given":"Felix","family":"M\u00f6lder","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen , Essen 45131,","place":["Germany"]},{"name":"Institute of Pathology, University Hospital Essen, University of Duisburg-Essen , Essen 45147,","place":["Germany"]}]},{"given":"Johannes","family":"K\u00f6ster","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Oncology, Institute for AI in Medicine (IKIM), University Hospital Essen, University of Duisburg-Essen , Essen 45131,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2025,12,14]]},"reference":[{"key":"2026010711363311000_btaf663-B1","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1002\/humu.24360","article-title":"Clinical exome sequencing\u2014mistakes and caveats","volume":"43","author":"Corominas","year":"2022","journal-title":"Hum Mutat"},{"key":"2026010711363311000_btaf663-B2","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026010711363311000_btaf663-B3","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"The bioconda team, and J. 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