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<p>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 <span>Lcptools</span> and introduce <span>LCPan</span>, an efficient variation graph constructor, which we show generates variation graphs &gt;12<InlineEquation ID="IEq1"><EquationSource Format="TEX">\(\times\)</EquationSource><EquationSource Format="MATHML"><math><mo>×</mo></math></EquationSource></InlineEquation> faster than <Emphasis FontCategory="NonProportional">vg</Emphasis>, while using &gt;13<InlineEquation ID="IEq2"><EquationSource Format="TEX">\(\times\)</EquationSource><EquationSource Format="MATHML"><math><mo>×</mo></math></EquationSource></InlineEquation> less memory.</p>

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LCPan: efficient variation graph construction using locally consistent parsing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年4月24日

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  • Akmuhammet Ashyralyyev,
  • Zülal Bingöl,
  • Begüm Filiz Öz,
  • Kaiyuan Zhu,
  • Salem Malikic,
  • Uzi Vishkin,
  • S. Cenk Sahinalp,
  • Can Alkan

摘要

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.