LightAlign: a lightweight pairwise aligner for memory-constrained HiFi read assembly

Abstract

IntroductionCurrent de novo genome assembly tools often demand substantial memory resources, and their execution typically relies on high-performance computing (HPC) clusters. This dependency limits their use in resource-constrained settings. Furthermore, mainstream third-generation sequencing assembly and alignment tools usually require explicit detection of overlap regions between reads, a process that often entails significant computational and storage overhead. ResultsTo address this issue, we developed LightAlign, a lightweight alignment tool for HiFi data that innovatively uses sequence-derived fuzzy features and reduces the peak memory usage during overlap detection. ConclusionsWhen combined with miniasm, LightAlign generated bacterial draft assemblies while maintaining peak memory usage below 1 GB and completed overlap generation for the tested eukaryotic datasets within 1.88 GB RAM.