Wenjie Wei, Songtao Gui, Jian Yang, Erik Garrison, Jianbing Yan, Hai-Jun Liu
{"title":"wgatools: an ultrafast toolkit for manipulating whole genome alignments.","authors":"Wenjie Wei, Songtao Gui, Jian Yang, Erik Garrison, Jianbing Yan, Hai-Jun Liu","doi":"","DOIUrl":null,"url":null,"abstract":"<p><strong>Summary: </strong>With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed <i>wgatools</i>, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment (WGA) formats, offering practical tools for conversion, processing, statistical evaluation, and visualization of alignments, thereby facilitating population-level genome analysis and advancing functional and evolutionary genomics.</p><p><strong>Availability and implementation: </strong><i>wgatools</i> 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. <i>wgatools</i> 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.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419180/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ArXiv","FirstCategoryId":"1085","ListUrlMain":"","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Summary: 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 (WGA) formats, offering practical tools for conversion, processing, statistical evaluation, and visualization of alignments, thereby facilitating population-level genome analysis and advancing functional and evolutionary genomics.
Availability and implementation: 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.