Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.

ABSTRACT:

Motivation

Strain-level microbiome profiling has revealed key insights into microbial community composition and strain dynamics. However, accurate strain-level analysis remains challenging due to limited linkage information, ambiguous read mapping, and complicating factors such as genome similarity, sequencing depth, and community complexity. These challenges are especially pronounced for short-read metagenomic data when estimating the relative abundances of multiple strains, a task critical for genotype-phenotype association studies.

Results

To address this gap, we present Strainify, which enables accurate strain-level abundance estimation from short-read metagenomes with as little as 1% genome coverage. Specifically, Strainify combines (1) identification of informative var

SUBMITTER: Luo RS 

PROVIDER: S-EPMC12632758 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature