Before revision:  Here we present an overview of metagenomics methods with a discussion of computational challenges and limitations . Our review covers clinical applications and presents applications for strain identification of Mycobacterium tuberculosis (TB), identification of infectious agents in cases of encephalitis, biomarkers for Inflammatory Bowel Disease, and explores the challenges of sampling the microbiome in various tissues. Our review also summarizes 11 of the most recent clinical metagenomics studies and discusses their commonalities and unique features .
After revision:  Here we present an overview of metagenomics methods with a discussion of computational challenges and limitations .