The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
Mg-RAST (metagenomics Rapid Annotation using Subsystem Technology) provides a web-accessible suite of tools for visualisation and analysis of metagenomic sequence data. Users are required to register. Data and analysis will remain private, unless the user enables public accessibility. Mg-RAST is primarily used for the annotation of shotgun sequences, allowing taxonomic and functional classification of metagenome data and comparison between metagenomes. It also supports amplicon sequence set analysis and metatranscriptomics. Mg-RAST for the impatient provides a user friendly introduction to the tools available.
QIIME (Quantitative Insights Into Microbial Ecology) is a bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. It aims to take the user from raw sequencing data through to publication quality statistics and figures.
IMG is a resource provided by JGI to annotate, analyse and integrate genomes and metagenomes. There are specific IMG data marts for analysis of biosynthetic genes and secondary metabolism, human microbiome samples and there is also the possibility of expert review of private genomes.