This document illustrates the workflow of shotgun metagenomic sequence data processing of hostderived microbiome and environmental metagenomes. This document specifies the requirements for quality control of shotgun metagenomic sequence data processing for massively parallel DNA sequencing. This document provides guidelines for data directory, data archive and metadata for shotgun metagenomic sequence data. This document applies to data storage, sharing and interoperability of shotgun metagenomic sequence data. This document applies to shotgun metagenomic sequence data processing and analyses, but excludes functional analysis.