{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T17:56:16Z","timestamp":1790963776318,"version":"4.1.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T00:00:00Z","timestamp":1770163200000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology","doi-asserted-by":"publisher","award":["BT\/GenomeIndia\/2018"],"award-info":[{"award-number":["BT\/GenomeIndia\/2018"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Nuclear mitochondrial DNA segments (NuMTs) can contribute to cancer development and disease progression by disrupting protein-coding genes. Furthermore, their presence confounds mitochondrial variant detection, underscoring the critical need for robust NuMT detection. Current methods to call NuMTs rely on short-read sequencing data but struggle to resolve complex NuMTs. These limitations can be overcome by employing long-read sequencing data. However, no such workflow exists to capture NuMTs from long-read sequencing data. Here, we introduce ANOMALY, a novel, easy-to-use workflow for detecting NuMTs from long-read sequencing data. The pipeline takes raw sequencing or aligned data and calls and visualises sample NuMTs. On 50 simulated datasets, the pipeline demonstrated high accuracy, with a precision of 1.000, a recall of 0.989, and an F1-score of 0.994. The pipeline underscores the limitations of short-read data in resolving and capturing complex NuMTs while demonstrating that long-read data enables their accurate identification. The Snakemake pipeline employs Python, Bash and R and is published under an open-source GNU GPL v3 license. Detailed information on setting up and running the pipeline, along with the source code, is available at https:\/\/github.com\/Nirmal2310\/ANOMALY.<\/jats:p>","DOI":"10.1093\/nargab\/lqag014","type":"journal-article","created":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T12:44:27Z","timestamp":1769172267000},"source":"Crossref","is-referenced-by-count":1,"title":["ANOMALY: a Snakemake pipeline for identifying NuMTs from long-read sequencing data"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6296-0494","authenticated-orcid":false,"given":"Nirmal S","family":"Mahar","sequence":"first","affiliation":[{"name":"Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi , New Delhi 110016 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachit","family":"Singh","sequence":"additional","affiliation":[{"name":"Centre for Brain Research, Indian Institute of Science , Bangalore 560012 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ishaan","family":"Gupta","sequence":"additional","affiliation":[{"name":"Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi , New Delhi 110016 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shweta","family":"Ramdas","sequence":"additional","affiliation":[{"name":"Centre for Brain Research, Indian Institute of Science , Bangalore 560012 ,","place":["India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,2,4]]},"reference":[{"key":"2026020405190205700_B1","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1016\/j.tig.2005.09.004","article-title":"Origin, evolution and genetic effects of nuclear insertions of organelle DNA","volume":"21","author":"Leister","year":"2005","journal-title":"Trends 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