Efficient variation graph construction using locally consistent parsing

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 (e.g., “cores”), ensuring consistency across partitions. Labeling the cores of an input string consistently not only provides a compact representation of the input but also enables the reapplication of LCP to refine the cores over multiple iterations, providing a progressively longer and more informative set of substrings for downstream analyses. We present the first iterative implementation of LCP with Lcptools and demonstrate its effectiveness in identifying cores with minimal collisions. Experimental results show that the number of cores at the ith iteration is O(n/ci) for c ∼ 2.34, while the average length and the average distance between consecutive cores are O(ci). Compared to the popular sketching techniques, LCP produces significantly fewer cores, enabling a more compact representation and faster analyses. To demonstrate the advantages of LCP in genomic string processing in terms of computation and memory efficiency, we also introduce LCPan, an efficient variation graph constructor. We show that LCPan generates variation graphs >10× faster than vg, while using >13× less memory.