Linking Clostridium difficile genome structure, microbiome composition, and host metabolomic signatures to disease severity in a pediatric inflammatory bowel disease cohort. Clostridioides difficile

C. difficile strains were isolated from 27 samples and sequenced using both the OxfordNanopore MinION and Illumina sequencing platforms. Hybrid assemblies were generated using an in-house pipeline named nanoflow (available at github.com/zhaoc1/nanoflow). Two samples were analyzed twice.