Taming large-scale genomic analyses via sparsified genomics.

ABSTRACT: Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, re

SUBMITTER: Alser M 

PROVIDER: S-EPMC11751491 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature