This technical specification details the requirements, and provides guidance for the application of advanced sequencing procedures for direct identification and characterisation without culturing of microbial causes of human infectious disease; sometimes termed clinical metagenomics. This document covers considerations associated with specimen collection, processing, nucleic acid isolation, targeting/enrichment, modification/manipulation, library preparation, sequencing, sequence analysis and reporting for the examination of sequences from microbes (including viruses, bacteria, protists and fungi) directly from human specimens (including blood, urine, cerebral spinal fluid and swabs in appropriate buffer) for the purposes of diagnosis, management and/or epidemiological monitoring of infectious disease. This document is applicable to institutions, e.g. medical diagnostic and public health laboratories, that use sequencing methods to detect clinical microbial pathogens as well as the biotechnology and IVD industry that serves them and those tasked with regulating their application. Sequencing intended to interrogate the genomes of cultured isolates, host derived nucleic acids or to comprehensively profile the microbiome (such as for estimating diversity indices) is not covered by this document. While there are shared considerations that will be accounted for, this document is not intended to directly cover microbial detection from the environment or foods furthermore, while not directly intended for veterinary applications many considerations detailed here will apply to broader one health considerations associated with animal disease.