Raw sequencing read archives hosted by the International Nucleotide Sequence Database Collaboration (GenBank, DDBJ and EMBL) serve as primary depository for an increasing stream of data generated by Next Generation Sequencing technologies. They currently host several tens of thousands of raw amplicon datasets. One half of these samples derive from human, mice and other animal hosts, while the rest originates from various environmental sources. In order to utilize this accumulating pool of sequence knowledge, we developed imngs, a platform that uniformly and systematically screens for, retrieves, processes, and analyzes all available prokaryotic 16S rRNA gene amplicon datasets and use them to build sample-specific sequence databases and OTU-based profiles. The retrieved information can be used to address questions of relevance in microbial ecology, for example with respect to the occurrence of specific microorganisms in different ecosystems or to perform targeted diversity studies. For better comparison with existing data, imngs also offers a complete pipeline for de novo analysis of users’ own raw amplicon sequencing data generated using the Illumina technology.