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

Although several tools exist for prokaryotic genome correction, most depend on external read mappers that impose computational overhead and usability barriers, leaving a need for fast, accurate, standalone solutions. We present ProGenFixer, a mapping-free tool that identifies and corrects errors in prokaryotic genomes using next-generation sequencing data. ProGenFixer compares k-mer profiles between an input genome and sequencing reads to pinpoint discrepancies, then applies a local assembly-based algorithm with a conservative correction strategy suited to refining high-quality reference genomes. In benchmarking, ProGenFixer ran over 5× faster than the existing tools tested while maintaining higher accuracy. Against slower but highly accurate tools, it showed comparable accuracy while running >17× faster, with better performance on long indels (>10 bp). ProGenFixer is designed primarily for conservative updating of already curated reference sequences rather than aggressive polishing of draft assemblies; accordingly, it does not automatically replace a reference base when substantial read support exists for both the reference and alternate alleles. Comparisons using 3 real bacterial resequencing datasets showed that most tool-specific disagreements occurred at mixed-support or low-depth sites, emphasizing that correction aggressiveness and accuracy are not equivalent in this application. ProGenFixer is implemented in C and runs as a standalone program with no external dependencies. The software is freely available at https://github.com/Scilence2022/ProGenFixer. A companion web platform is available at https://progenfixer.biodesign.ac.cn.