Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.
复制标题
通过系统发育压缩对微生物基因组进行高效、稳健的搜索。
DOI：
10.1101/2023.04.15.536996
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Baym,Michael
中科院分区：
文献类型：
--
作者：
Břinda,Karel;Lima,Leandro;Pignotti,Simone;Quinones-Olvera,Natalia;Salikhov,Kamil;Chikhi,Rayan;Kucherov,Gregory;Iqbal,Zamin;Baym,Michael
接近数百万个测序基因组的综合集合已成为生命科学的核心信息源。然而，这些集合的快速增长使得使用基本局部对齐搜索工具 (BLAST) 及其后继者等工具实际上不可能搜索这些数据。在这里，我们提出了一种称为系统发育压缩的技术，该技术使用进化历史来指导压缩，并使用现有算法和数据结构有效地搜索大量微生物基因组。我们表明，当应用于接近数百万个基因组的现代多样化集合时，无损系统发育压缩可以将程序集、de Bruijn 图和 k-mer 索引的压缩率提高一到两个数量级。此外，我们开发了一个管道，用于对这些系统发育压缩的参考数据进行类似 BLAST 的搜索，并证明它可以在几个小时内在普通台式计算机上将基因、质粒或整个测序实验与 2019 年之前的所有已测序细菌进行比对。系统发育压缩在计算生物学中具有广泛的应用，并可能为未来的基因组学基础设施提供基本的设计原则。
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 the Basic Local Alignment Search Tool (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 andk-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.