The MIQ Score System is an easily extensible system that contains a fully-automated, containerized microbiomics pipeline for comparing observed read abundances to expected values from a standardized microbial community with known relative abundances and manufacturing tolerances. This system is designed to be rapidly deployed through Docker in a highly-reproducible manner across different computing infrastructures and requires only information on the raw sequencing reads as input to generate a detailed report scoring accuracy relative to the standard and providing several figures that can help identify potential biases in microbiome preparation.