{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,18]],"date-time":"2026-01-18T03:06:52Z","timestamp":1768705612656,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T00:00:00Z","timestamp":1595548800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100005289","name":"NIJ","doi-asserted-by":"publisher","award":["2017-DN-BX-0134"],"award-info":[{"award-number":["2017-DN-BX-0134"]}],"id":[{"id":"10.13039\/100005289","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/Ahhgust\/RtN<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa642","type":"journal-article","created":{"date-parts":[[2020,7,18]],"date-time":"2020-07-18T11:10:07Z","timestamp":1595070607000},"page":"5115-5116","source":"Crossref","is-referenced-by-count":25,"title":["Numt identification and removal with RtN!"],"prefix":"10.1093","volume":"36","author":[{"given":"August E","family":"Woerner","sequence":"first","affiliation":[{"name":"Department of Microbiology, Immunology and Genetics"},{"name":"Center for Human Identification, University of North Texas Health Science Center (UNTHSC) , Fort Worth, TX 76107, USA"}]},{"given":"Jennifer Churchill","family":"Cihlar","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Genetics"},{"name":"Center for Human Identification, University of North Texas Health Science Center (UNTHSC) , Fort Worth, TX 76107, USA"}]},{"given":"Utpal","family":"Smart","sequence":"additional","affiliation":[{"name":"Center for Human Identification, University of North Texas Health Science Center (UNTHSC) , Fort Worth, TX 76107, USA"}]},{"given":"Bruce","family":"Budowle","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Genetics"},{"name":"Center for Human Identification, University of North Texas Health Science Center (UNTHSC) , Fort Worth, TX 76107, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,7,24]]},"reference":[{"key":"2023062408113367300_btaa642-B1","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-6-S4-S4","article-title":"HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research","volume":"6","author":"Attimonelli","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023062408113367300_btaa642-B2","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1111\/1556-4029.12441","article-title":"Simultaneous detection of human mitochondrial DNA and nuclear-inserted mitochondrial-origin sequences (NumtS) using forensic mtDNA amplification strategies and pyrosequencing technology","volume":"59","author":"Bintz","year":"2014","journal-title":"J. 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Mol. Evol"},{"key":"2023062408113367300_btaa642-B10","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/elps.201800135","article-title":"Bioinformatic removal of NUMT-associated variants in mitotiling NGS data from whole blood samples","volume":"39","author":"Ring","year":"2018","journal-title":"Electrophoresis"},{"key":"2023062408113367300_btaa642-B11","doi-asserted-by":"crossref","first-page":"S52","DOI":"10.1080\/00450618.2019.1569150","article-title":"MVC: an integrated mitochondrial variant caller for forensics","volume":"51","author":"Roth","year":"2019","journal-title":"Aust. J. Forensic Sci"},{"key":"2023062408113367300_btaa642-B12","doi-asserted-by":"crossref","first-page":"102146","DOI":"10.1016\/j.fsigen.2019.102146","article-title":"A novel phylogenetic approach for de novo discovery of putative nuclear mitochondrial (pNumt) haplotypes","volume":"43","author":"Smart","year":"2019","journal-title":"Forensic Sci. Int. 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