Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.

ABSTRACT: Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, and k -mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST

SUBMITTER: Brinda K 

PROVIDER: S-EPMC10153118 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature