QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters

With minimal parameter tuning, QIIME2 outperformed the R pipeline in taxonomic resolution, and improved reproducibility by provenance tracking. Our findings emphasize how bioinformatics pipeline choices impact nemabiome outputs including the number of species detected, ranks of abundant taxa, and alpha and beta diversities. We provide a reproducible and user-friendly QIIME2 workflow suitable for researchers seeking standardized analyses of ITS2 nemabiome data.