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bioRxiv · 10.64898/2026.07.30.741934

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

Liu, J.·Zhang, J.
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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.

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Liu, J., Zhang, J.. 2026-08-05. LightAlign: a lightweight pairwise aligner for memory-constrained HiFi read assembly. https://doi.org/10.64898/2026.07.30.741934

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