Signal enrichment with strain-level resolution in metagenomes using topological data analysis

摘要

BackgroundA metagenome is a collection of genomes, usually in a micro-environment, and sequencing a metagenomic sample en masse is a powerful means for investigating the community of the constituent microorganisms. One of the challenges is in distinguishing between similar organisms due to rampant multiple possible assignments of sequencing reads, resulting in false positive identifications. We map the problem to a topological data analysis (TDA) framework that extracts information from the geometric structure of data. Here the structure is defined by multi-way relationships between the sequencing reads using a reference database.