{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T00:58:46Z","timestamp":1771030726175,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2019,10,18]],"date-time":"2019-10-18T00:00:00Z","timestamp":1571356800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771479"],"award-info":[{"award-number":["31771479"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81822036"],"award-info":[{"award-number":["81822036"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31770931"],"award-info":[{"award-number":["31770931"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science Fund for Creative Research Groups of the NSFC","award":["81521003"],"award-info":[{"award-number":["81521003"]}]},{"name":"NSFC Projects of International Cooperation and Exchanges of NSFC","award":["61661146004"],"award-info":[{"award-number":["61661146004"]}]},{"name":"Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program","award":["2017BT01S131"],"award-info":[{"award-number":["2017BT01S131"]}]},{"name":"Municipal Planning Projects of Scientific Technology of Guangdong","award":["201804020083"],"award-info":[{"award-number":["201804020083"]}]},{"name":"Science and Technology Program of Guangzhou","award":["201400000004"],"award-info":[{"award-number":["201400000004"]}]},{"name":"National Natural Science Foundation of Guangdong","award":["2015B050501006"],"award-info":[{"award-number":["2015B050501006"]}]},{"name":"Team Program of Guangdong Natural Science Foundation","award":["2014A030312002"],"award-info":[{"award-number":["2014A030312002"]}]},{"name":"Thousand Talent Plan of China, and the Guangdong Natural Science Funds for Distinguished Young Scholar","award":["2017A030306030"],"award-info":[{"award-number":["2017A030306030"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.<\/jats:p>","DOI":"10.1093\/bib\/bbz092","type":"journal-article","created":{"date-parts":[[2019,10,15]],"date-time":"2019-10-15T21:25:12Z","timestamp":1571174712000},"page":"1706-1716","source":"Crossref","is-referenced-by-count":24,"title":["Tools for fundamental analysis functions of TCR repertoires: a systematic comparison"],"prefix":"10.1093","volume":"21","author":[{"given":"Yanfang","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"},{"name":"Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China"},{"name":"Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiujia","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"},{"name":"Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Minhui","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jin Xia","family":"Ou","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huikun","family":"Zeng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiaqi","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunhong","family":"Lan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"},{"name":"Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China"},{"name":"Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hong-Wei","family":"Zhou","sequence":"additional","affiliation":[{"name":"Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China"},{"name":"Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4310-0525","authenticated-orcid":false,"given":"Zhenhai","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China"},{"name":"Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China"},{"name":"Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China"},{"name":"Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,10,18]]},"reference":[{"key":"2021031109193828600_ref1","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nri1292","article-title":"The many important facets of T-cell repertoire diversity","volume":"4","author":"Nikolich-\u017dugich","year":"2004","journal-title":"Nat Rev Immuno"},{"key":"2021031109193828600_ref2","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1038\/s41598-018-19548-y","article-title":"Increased diversity with reduced \u201cdiversity evenness\u201d of tumor infiltrating T-cells 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