ProGenFixer: An Ultrafast and Accurate Tool for Correcting Prokaryotic Genome Sequences Using a Mapping-Free Algorithm

Abstract Although prokaryotic genomes are simpler, making variation analysis more straightforward, an efficient and user-friendly tool for their rapid sequence correction is lacking. We present ProGenFixer, an ultra-fast, mapping-free tool specifically designed to efficiently identify and correct errors in prokaryotic genomes using next-generation sequencing (NGS) data. ProGenFixer compares k -mer profiles between the reference genome and reads to pinpoint discrepancies, employs a local assembly-based algorithm to estimate corrected sequences, and automatically implements corrections. Benchmarking demonstrates ProGenFixer’s speed and accuracy advantages. It is over >5x faster than the swiftest existing tool tested while maintaining higher accuracy. Compared to slower, highly accurate tools, ProGenFixer shows comparable accuracy but is >17x faster and demonstrates enhanced performance on long indels (>10 bp). Implemented in C, ProGenFixer is a standalone, user-friendly tool offering a comprehensive solution for prokaryotic genome correction. The software is freely available at https://github.com/Scilence2022/ProGenFixer . Additionally, a companion web-based platform offering a ready-to-use interface can be accessed at https://progenfixer.biodesign.ac.cn .