LCPan: efficient variation graph construction using locally consistent parsing

Genome biology 2026 Open access

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Authors: Akmuhammet Ashyralyyev, Zülal Bingöl, Begüm Filiz Öz, Kaiyuan Zhu, Salem Malikić, Uzi Vishkin, Cenk Sahinalp, Can Alkan
DOI: 10.1186/s13059-026-04088-w
Cited by: 0
References: 50

Abstract

Abstract 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 , while using >13 $$\times$$ × less memory.

Fields of Study & Subjects

Genomics and Phylogenetic Studies Algorithms and Data Compression Genome Rearrangement Algorithms

Publication details

Journal / source
Genome biology
Publisher
Springer Science and Business Media LLC
Volume
27
Issue
1
Publication date
24 April 2026
Language
EN