QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.

ABSTRACT: Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-ca

SUBMITTER: Licata AG 

PROVIDER: S-EPMC12403817 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature