{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:22:03Z","timestamp":1787962923425,"version":"build-2784847793"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T00:00:00Z","timestamp":1736208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI151075"],"award-info":[{"award-number":["R01AI151075"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI158527"],"award-info":[{"award-number":["R01AI158527"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)\u2014the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with in vitro propagation. No single tool exists for the entirety of Ct genome assembly, necessitating the adaptation of multiple programs with varying success. Compounding this issue is the absence of reliable Ct reference strain genomes. We, therefore, developed CtGAP\u2014Chlamydia trachomatis \u00a0Genome Assembly Pipeline\u2014as an integrated \u2018one-stop-shop\u2019 pipeline for assembly and characterization of Ct genome sequencing data from various sources including isolates, in vitro samples, clinical swabs and urine. CtGAP, written in Snakemake, enables read quality statistics output, adapter and quality trimming, host read removal, de novo and reference-guided assembly, contig scaffolding, selective ompA, multi-locus-sequence and plasmid typing, phylogenetic tree construction, and recombinant genome identification. Twenty Ct reference genomes were also generated. Successfully validated on a diverse collection of 363 samples containing Ct, CtGAP represents a novel pipeline requiring minimal bioinformatics expertise with easy adaptation for use with other bacterial species.<\/jats:p>","DOI":"10.1093\/nargab\/lqae187","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T10:41:16Z","timestamp":1736246476000},"source":"Crossref","is-referenced-by-count":8,"title":["Whole-genome automated assembly pipeline for <i>Chlamydia trachomatis<\/i> strains from reference, <i>in vitro<\/i> and clinical samples using the integrated CtGAP pipeline"],"prefix":"10.1093","volume":"7","author":[{"given":"Olusola","family":"Olagoke","sequence":"first","affiliation":[{"name":"Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine , 550 16th Street, 4th Floor\u00a0Mission Hall,\u00a0 San Francisco,\u00a0CA ,\u00a094158,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ammar","family":"Aziz","sequence":"additional","affiliation":[{"name":"Victorian Infectious Diseases Reference Laboratory , 792 Elizabeth Street,\u00a0 Melbourne ,\u00a0 Victoria , 3000,\u00a0","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucile\u00a0H","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California San Francisco and\u00a0Berkeley School of Engineering , 306\u00a0Stanley\u00a0Hall,\u00a0 Berkeley ,\u00a0CA,\u00a094720,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8966-9680","authenticated-orcid":false,"given":"Timothy\u00a0D","family":"Read","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Genetics, Division of Infectious Diseases, Emory University School of Medicine , 100 Woodruff Circle,\u00a0 Atlanta , GA , 30322,\u00a0","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4490-1746","authenticated-orcid":false,"given":"Deborah","family":"Dean","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine , 550 16th Street, 4th Floor\u00a0Mission Hall,\u00a0 San Francisco,\u00a0CA ,\u00a094158,","place":["USA"]},{"name":"Department of Bioengineering, University of California San Francisco and\u00a0Berkeley School of Engineering , 306\u00a0Stanley\u00a0Hall,\u00a0 Berkeley ,\u00a0CA,\u00a094720,","place":["USA"]},{"name":"Bixby Center for Global Reproductive Health, University of California San Francisco , 1001 Potrero Ave,\u00a0 San Francisco , CA , 94110,\u00a0","place":["USA"]},{"name":"Benioff Center for Microbiome Medicine, University of California San Francisco , 513 Parnassus Avenue, S357,\u00a0 San Francisco , CA , 94143,\u00a0","place":["USA"]},{"name":"University of California San Francisco Institute of Global Health Sciences , 550 16th Street, 3rd Floor\u00a0Mission Hall,\u00a0 San Francisco , CA , 94158,\u00a0","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"2025030419180673900_B1","article-title":"Department of Reproductive Health and Research","volume-title":"Global Health Sector Strategy on Sexually Transmitted Infection 2016-2021: Towards ending STIs","author":"World Health Organization","year":"2016"},{"key":"2025030419180673900_B2","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1093\/infdis\/152.4.791","article-title":"Immunotyping of Chlamydia trachomatis with monoclonal antibodies","volume":"152","author":"Wang","year":"1985","journal-title":"J. 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