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However, most existing tools fail to provide comprehensive statistical results and exhibit limited performance gains from multithreading. Here, we present PanDepth, an ultra-fast and efficient tool for calculating coverage and depth from sequencing alignments. PanDepth outperforms other tools in computation time and memory efficiency for both BAM and CRAM-format alignment files from sequencing data, regardless of read length. It employs chromosome parallel computation and optimized data structures, resulting in ultrafast computation speeds and memory efficiency. It accepts sorted or unsorted BAM and CRAM-format alignment files as well as GTF, GFF and BED-formatted interval files or a specific window size. When provided with a reference genome sequence and the option to enable GC content calculation, PanDepth includes GC content statistics, enhancing the accuracy and reliability of copy number variation analysis. Overall, PanDepth is a powerful tool that accelerates scientific discovery in genomics research.<\/jats:p>","DOI":"10.1093\/bib\/bbae197","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T10:30:30Z","timestamp":1714732230000},"source":"Crossref","is-referenced-by-count":29,"title":["PanDepth, an ultrafast and efficient genomic tool for coverage calculation"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9449-654X","authenticated-orcid":false,"given":"Huiyang","family":"Yu","sequence":"first","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province , China"},{"name":"Key Laboratory for Vegetable Biology of Hunan Province, Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, College of Horticulture, Hunan Agricultural University , No. 1 Nongda Road, Furong District, Changsha, 410128, Hunan Province , China"}]},{"given":"Chunmei","family":"Shi","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0483-5390","authenticated-orcid":false,"given":"Weiming","family":"He","sequence":"additional","affiliation":[{"name":"BGI Research , Yumin street, Yazhou District, Sanya, 572025, Hainan Province , China"}]},{"given":"Feng","family":"Li","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province , China"}]},{"given":"Bo","family":"Ouyang","sequence":"additional","affiliation":[{"name":"National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University , No. 1 Shizishan Street, Hongshan District, Wuhan 430070, Hubei Province , China"}]}],"member":"286","published-online":{"date-parts":[[2024,5,2]]},"reference":[{"key":"2024050310302183100_ref1","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024050310302183100_ref2","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic 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