wgatools：一个用于操作全基因组比对的超快速工具包。

wgatools: an ultrafast toolkit for manipulating whole-genome alignments.

作者信息

Wei Wenjie, Gui Songtao, Yang Jian, Garrison Erik, Yan Jianbing, Liu Hai-Jun

机构信息

School of Life Sciences, Westlake University, Hangzhou 310030, China.

National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.

出版信息

Bioinformatics. 2025 Mar 29;41(4). doi: 10.1093/bioinformatics/btaf132.

DOI:10.1093/bioinformatics/btaf132

PMID:40152239

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11978383/

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 formats, offering practical tools for conversion, processing, 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 and https://zenodo.org/records/14882797.

摘要

随着长读长测序技术的快速发展，个体完整基因组时代即将来临。我们开发了wgatools，这是一个跨平台的超快速工具包，支持一系列全基因组比对格式，提供用于比对的转换、处理、评估和可视化的实用工具，从而促进群体水平的基因组分析，并推动功能基因组学和进化基因组学的发展。

可用性与实现

wgatools支持多种格式，能够处理、过滤和统计评估比对，基于比对进行变异检测，并在本地和全基因组范围内可视化比对。它采用Rust构建，以提高效率并安全使用内存，确保快速性能，能够处理由数百个基因组组成的大型数据集。wgatools作为免费软件根据MIT开源许可发布，其源代码可在https://github.com/wjwei-handsome/wgatools和https://zenodo.org/records/14882797上免费获取。