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Although protozoan parasites cause serious diseases in humans and animals, WGS data on them are relatively scarce due to the large genomes and lack of cultivation techniques for some. In this review, we have illustrated bioinformatic analyses of WGS data and their applications in studies of the genomic epidemiology of apicomplexan parasites. WGS has been used in outbreak detection and investigation, studies of pathogen transmission and evolution, and drug resistance surveillance and tracking. However, comparative analysis of parasite WGS data is still in its infancy, and available WGS data are mainly from a few genera of major public health importance, such as\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    ,\n                    <jats:italic>Toxoplasma<\/jats:italic>\n                    , and\n                    <jats:italic>Cryptosporidium<\/jats:italic>\n                    . In addition, the utility of third\u2010generation sequencing technology for complete genome assembly at the chromosome level, studies of the biological significance of structural genomic variation, and molecular surveillance of pathogens has not been fully exploited. These issues require large\u2010scale WGS of various protozoan parasites of public health and veterinary importance using both second\u2010 and third\u2010generation sequencing technologies.\n                  <\/jats:p>","DOI":"10.1155\/2024\/7679727","type":"journal-article","created":{"date-parts":[[2024,6,8]],"date-time":"2024-06-08T08:18:19Z","timestamp":1717834699000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Analytic Approaches in Genomic Epidemiological Studies of Parasitic Protozoa"],"prefix":"10.1155","volume":"2024","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7337-5191","authenticated-orcid":false,"given":"Tianpeng","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory for Animal Disease Control and Prevention South China Agricultural University  Guangzhou 510642 China  scau.edu.cn"},{"name":"Guangdong Provincial Key Laboratory of Utilization and Conservation of 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