{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T10:19:30Z","timestamp":1768817970191,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T00:00:00Z","timestamp":1743033600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Framework Programme for Research and Innovation Horizon 2020"},{"name":"Marie Curie Sk\u0142odowska Grant Agreement","award":["847548"],"award-info":[{"award-number":["847548"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole-genome alignment formats, offering practical tools for conversion, processing, evaluation, and visualization of alignments, thereby facilitating population-level genome analysis and advancing functional and evolutionary genomics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>wgatools supports diverse formats and can process, filter, and statistically evaluate alignments, perform alignment-based variant calling, and visualize alignments both locally and genome-wide. Built with Rust for efficiency and safe memory usage, it ensures fast performance and can handle large datasets consisting of hundreds of genomes. wgatools is published as free software under the MIT open-source license, and its source code is freely available at https:\/\/github.com\/wjwei-handsome\/wgatools and https:\/\/zenodo.org\/records\/14882797.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf132","type":"journal-article","created":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T23:53:06Z","timestamp":1744156386000},"source":"Crossref","is-referenced-by-count":5,"title":["<i>wgatools<\/i>: an ultrafast toolkit for manipulating whole-genome alignments"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4105-9693","authenticated-orcid":false,"given":"Wenjie","family":"Wei","sequence":"first","affiliation":[{"name":"School of Life Sciences, Westlake University , Hangzhou 310030,","place":["China"]},{"name":"National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , Wuhan 430070,","place":["China"]}]},{"given":"Songtao","family":"Gui","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University , Tai\u2019an 271018,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2001-2474","authenticated-orcid":false,"given":"Jian","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Westlake University , Hangzhou 310030,","place":["China"]},{"name":"Westlake Laboratory of Life Sciences and Biomedicine , Hangzhou 310024,","place":["China"]}]},{"given":"Erik","family":"Garrison","sequence":"additional","affiliation":[{"name":"Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center , Memphis, TN 38163,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8650-7811","authenticated-orcid":false,"given":"Jianbing","family":"Yan","sequence":"additional","affiliation":[{"name":"National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , Wuhan 430070,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7717-893X","authenticated-orcid":false,"given":"Hai-Jun","family":"Liu","sequence":"additional","affiliation":[{"name":"Yazhouwan National Laboratory , Sanya 572024,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,3,27]]},"reference":[{"key":"2025041602170698400_btaf132-B1","first-page":"121","volume-title":"Whole-Genome Alignment","author":"Dewey","year":"2019"},{"key":"2025041602170698400_btaf132-B2","unstructured":"Guarracino A. \u00a0Andreaguarracino\/paf2chain: v0.1.0. Zenodo \u00a02023. 10.5281\/zenodo.8108447"},{"key":"2025041602170698400_btaf132-B3","author":"Guarracino","year":"2023"},{"key":"2025041602170698400_btaf132-B4","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1093\/bioinformatics\/btt128","article-title":"HAL: a hierarchical format for storing and analyzing multiple genome alignments","volume":"29","author":"Hickey","year":"2013","journal-title":"Bioinformatics"},{"key":"2025041602170698400_btaf132-B5","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/s13059-022-02735-6","article-title":"Multiple genome alignment in the telomere-to-telomere assembly era","volume":"23","author":"Kille","year":"2022","journal-title":"Genome Biol"},{"key":"2025041602170698400_btaf132-B6","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2025041602170698400_btaf132-B7","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1038\/s41576-024-00718-w","article-title":"Genome assembly in the telomere-to-telomere era","volume":"25","author":"Li","year":"2024","journal-title":"Nat Rev Genet"},{"key":"2025041602170698400_btaf132-B8","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.tplants.2023.08.013","article-title":"New whole-genome alignment tools are needed for tapping into plant diversity","volume":"29","author":"Song","year":"2024","journal-title":"Trends Plant Sci"},{"key":"2025041602170698400_btaf132-B9","doi-asserted-by":"crossref","first-page":"e2113075119","DOI":"10.1073\/pnas.2113075119","article-title":"Anchorwave: sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication","volume":"119","author":"Song","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025041602170698400_btaf132-B10","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.tig.2018.05.008","article-title":"The third revolution in sequencing technology","volume":"34","author":"van Dijk","year":"2018","journal-title":"Trends Genet"},{"key":"2025041602170698400_btaf132-B11","doi-asserted-by":"publisher","DOI":"10.1101\/2024.07.31.605654,"},{"key":"2025041602170698400_btaf132-B12","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1186\/s12864-024-10430-y","article-title":"ACMGA: a reference-free multiple-genome alignment pipeline for plant species","volume":"25","author":"Zhou","year":"2024","journal-title":"BMC Genomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/4\/btaf132\/62786131\/btaf132.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/4\/btaf132\/62786131\/btaf132.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,16]],"date-time":"2025-04-16T06:17:26Z","timestamp":1744784246000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf132\/8098043"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,3,27]]},"references-count":12,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,3,29]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf132","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,4]]},"published":{"date-parts":[[2025,3,27]]},"article-number":"btaf132"}}