wgatools: an ultrafast toolkit for manipulating whole genome alignments

TL;DR

wgatools is a fast, cross-platform toolkit designed for efficient manipulation, analysis, and visualization of whole genome alignments, supporting large datasets and multiple formats to facilitate genomics research.

Contribution

It introduces a Rust-based, ultrafast toolkit that supports diverse WGA formats and provides comprehensive tools for processing, evaluation, and visualization of genome alignments.

Findings

Supports processing of hundreds of genomes efficiently

Enables detailed statistical evaluation of alignments

Provides visualization tools for genome-wide analysis

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. Contact: weiwenjie@westlake.edu.cn (W.W.) or liuhaijun@yzwlab.cn (H.-J.L.).