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However, the characteristics of faecal DNA sequencing, particularly the relationship between sequencing volume and genotyping accuracy or genomic coverage, have remained unclear. This knowledge gap makes it challenging to pre\u2010estimate the required sequencing depth to ensure data quality while controlling costs. In this study, we used host\u2010enriched faecal DNA obtained via peri\u2010extraction enrichment by SDS (PEERS) to perform comparative analyses of whole\u2010genome sequencing data from paired faecal and blood samples of 11 captive Amur tigers. We systematically evaluated how data volume affects genomic coverage and genotyping accuracy. Our results revealed that faecal sequencing reads cover the genome unevenly, which may compromise the reliability of underrepresented allele identification and subsequent genomic analyses. Specifically, genomic coverage and genotyping accuracy, including\n                    <jats:italic>precision<\/jats:italic>\n                    ,\n                    <jats:italic>error rate<\/jats:italic>\n                    ,\n                    <jats:italic>recall<\/jats:italic>\n                    and\n                    <jats:italic>F<\/jats:italic>\n                    1\u2010\n                    <jats:italic>score<\/jats:italic>\n                    , improved with increasing sequencing depth in both blood and faecal DNA. For reliable genotyping (values &gt;\u20090.95), a minimum average depth of 20\u00d7 was required for blood\u2010derived DNA, whereas faecal DNA needed up to 50\u00d7 depth when the nuclear DNA enrichment efficiency (\n                    <jats:italic>EE<\/jats:italic>\n                    <jats:sub>N<\/jats:sub>\n                    , defined as the ratio of nuclear to bacterial DNA copy number) reached 5E\u20105. At this sequencing volume, population\u2010level indices, such as nucleotide diversity (\u03c0), polymorphism information content (PIC), the distribution of \u03c0 in 500\u2010kb sliding windows and SNP density, as well as individual\u2010level indices, including heterozygosity, kinship coefficients, inbreeding coefficient (\n                    <jats:italic>F<\/jats:italic>\n                    <jats:sub>ROH<\/jats:sub>\n                    ) and genetic load, were highly consistent between faecal and blood samples. Only observed heterozygosity (\n                    <jats:italic>H<\/jats:italic>\n                    o) and kernel density distributions of minor allele frequency (MAF) showed slight discrepancies. These findings underscore that effective host DNA enrichment using PEERS combined with deep sequencing is essential to achieve adequate genomic coverage and accurate genotyping when utilising faecal samples. Monitoring enrichment efficiency can help determine the necessary sequencing depth, facilitating cost\u2010effective experimental design. This study offers practical guidance for the application of faecal DNA in genomic research and supports the broader use of this non\u2010invasive material in future wildlife studies.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.70120","type":"journal-article","created":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T23:17:32Z","timestamp":1773011852000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Assessment of High Throughput Sequencing Quality of Host\n                    <scp>DNA<\/scp>\n                    Enriched From Faeces: A Case From Captive Tiger"],"prefix":"10.1111","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-6665-5822","authenticated-orcid":false,"given":"Jincheng","family":"Yang","sequence":"first","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4378-6053","authenticated-orcid":false,"given":"Le","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangyu","family":"Cui","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haitao","family":"Xu","sequence":"additional","affiliation":[{"name":"Heilongjiang Siberian Tiger Park  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"},{"name":"State Forestry and Grassland Administration Detecting Centre of Wildlife  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lulu","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6009-2377","authenticated-orcid":false,"given":"Mengjia","family":"Yu","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth Kamili","family":"Mtui","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"},{"name":"College of African Wildlife Management  Mweka Tanzania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaotong","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"},{"name":"Heze Center for Disease Control and Prevention  Heze China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianing","family":"Chu","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ao","family":"Zou","sequence":"additional","affiliation":[{"name":"College of Wildlife and Protected Area Northeast Forestry University  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Liu","sequence":"additional","affiliation":[{"name":"Heilongjiang Siberian Tiger Park  Harbin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lifeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Science and Technology Research Center of China Customs  Beijing 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