{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T14:25:18Z","timestamp":1784039118160,"version":"3.55.0"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T00:00:00Z","timestamp":1738368000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["218328"],"award-info":[{"award-number":["218328"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>\u201ctidk\u201d (short for telomere identification toolkit) uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. \u201ctidk\u201d is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The \u201ctidk\u201d Rust crate is freely available under the MIT license (https:\/\/crates.io\/crates\/tidk), and the source code is available at https:\/\/github.com\/tolkit\/telomeric-identifier.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf049","type":"journal-article","created":{"date-parts":[[2025,2,1]],"date-time":"2025-02-01T05:30:47Z","timestamp":1738387847000},"source":"Crossref","is-referenced-by-count":123,"title":["tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2561-516X","authenticated-orcid":false,"given":"Max R","family":"Brown","sequence":"first","affiliation":[{"name":"School of Life Sciences, Anglia Ruskin University , Cambridge, CB1 1PT,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pablo","family":"Manuel Gonzalez de La Rosa","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute , Hinxton, CB10 1RQ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Blaxter","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute , Hinxton, CB10 1RQ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,31]]},"reference":[{"key":"2025030422240157800_btaf049-B1","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1093\/molbev\/msh180","article-title":"TAHRE, a novel telomeric retrotransposon from Drosophila melanogaster, reveals the origin of Drosophila telomeres","volume":"21","author":"Abad","year":"2004","journal-title":"Mol Biol Evol"},{"key":"2025030422240157800_btaf049-B2","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.mrrev.2005.12.003","article-title":"Telomeres, interstitial telomeric repeat sequences, and chromosomal aberrations","volume":"612","author":"Bolz\u00e1n","year":"2006","journal-title":"Mutat Res"},{"key":"2025030422240157800_btaf049-B3","doi-asserted-by":"crossref","first-page":"evae001","DOI":"10.1093\/gbe\/evae001","article-title":"Chromosome-level genome assembly and annotation of a periodical cicada species: Magicicada septendecula","volume":"16","author":"Bush","year":"2024","journal-title":"Genome Biol Evol"},{"key":"2025030422240157800_btaf049-B4","doi-asserted-by":"crossref","first-page":"78","DOI":"10.12688\/wellcomeopenres.18986.1","article-title":"The genome sequence of the Forest Cuckoo Bee, Bombus sylvestris (Lepeletier, 1832)","volume":"8","author":"Crowley","year":"2023","journal-title":"Wellcome Open Res"},{"key":"2025030422240157800_btaf049-B5","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2115642118","article-title":"Sequence locally, think globally: the Darwin tree of life project","volume":"119","author":"Darwin Tree of Life Project Consortium","year":"2022","journal-title":"Proc Natl Acad Sci"},{"key":"2025030422240157800_btaf049-B6","doi-asserted-by":"crossref","first-page":"000568","DOI":"10.1099\/acmi.0.000568.v3","article-title":"Genome assembly of a biocontrol agent of insect agricultural pests","volume":"5","author":"Erdos","year":"2023","journal-title":"Access Microbiol"},{"key":"2025030422240157800_btaf049-B7","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1186\/s12859-019-2851-0","article-title":"TelomereHunter\u2014in silico estimation of telomere content and composition from cancer genomes","volume":"20","author":"Feuerbach","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2025030422240157800_btaf049-B8","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1093\/bioinformatics\/btv573","article-title":"Rust-Bio: a fast and safe bioinformatics library","volume":"32","author":"K\u00f6ster","year":"2016","journal-title":"Bioinformatics"},{"key":"2025030422240157800_btaf049-B9","first-page":"1242","article-title":"Telomere functions. 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