
==== Front
ArXiv
ArXiv
arxiv
ArXiv
2331-8422
Cornell University

arXiv:2409.08569v1
2409.08569
1
preprint
Article
wgatools: an ultrafast toolkit for manipulating whole genome alignments
Wei Wenjie
Gui Songtao
Yang Jian
Garrison Erik
Yan Jianbing
Liu Hai-Jun
13 9 2024
arXiv:2409.08569v1https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://arxiv.org/abs/2409.08569v1
nihpp-2409.08569v1.pdf
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. Contact: weiwenjie@westlake.edu.cn (W.W.) or liuhaijun@yzwlab.cn (H.-J.L.).
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