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LCPan: efficient variation graph construction using locally consistent parsing
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DOI：10.1186/s13059-026-04088-w.png)
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Abstract
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Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (“cores”), ensuring consistency across partitions. Compared to the popular sketching techniques, LCP produces fewer cores, enabling a more compact representation and faster analyses. Here, we present the first iterative implementation of LCP with Lcptools and introduce LCPan, an efficient variation graph constructor, which we show generates variation graphs >12$$\times$$ faster than vg, while using >13$$\times$$ less memory.
Keywords:
Locally consistent parsing
Genome representation
Variation graph
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