RT Journal Article
SR Electronic
T1 Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.04.15.536996
DO 10.1101/2023.04.15.536996
A1 Břinda, Karel
A1 Lima, Leandro
A1 Pignotti, Simone
A1 Quinones-Olvera, Natalia
A1 Salikhov, Kamil
A1 Chikhi, Rayan
A1 Kucherov, Gregory
A1 Iqbal, Zamin
A1 Baym, Michael
YR 2024
UL http://biorxiv.org/content/early/2024/05/11/2023.04.15.536996.abstract
AB 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-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.Competing Interest StatementThe authors have declared no competing interest.