Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.

ABSTRACT: Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome using various metagenomic mapping tools or human reference genomes, followed by filtration before metagenomic analysis. In this study, we conducted a comprehensive analysis to identify the optimal combination of alignment software and human reference genomes using benchmarking data. Our findings show that the combination of bwa-mem and the telomere-to-telomere human genome (CHM13-T2T) is the most effective in removing human reads in simulated data. We also analyzed CHM13-T2T-derived sequences in RefSeq to understand how CHM13-T2T reduces false positive resu

SUBMITTER: Liu D 

PROVIDER: S-EPMC12542756 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature