IMG Group

The Integrated Microbial Genomes group is focused on: 

• Developing state-of-the-art data processing and analysis pipelines for the interpretation of microbiome omics data
• Developing forward-looking strategies for the deployment of computational workflows at peta- and exa- scales on multicore and many core architectures with the ultimate objective of facilitating omics-based scientific investigations.
• Development and maintenance of the Integrated Microbial Genomes (IMG) data management system

As part of this project, pairwise average nucleotide identities (ANI) and fraction of orthologous genomic regions (Alignment fraction, AF) have been computed for nearly 28,000 bacterial and archaeal genomes. By clustering genomes based on their pairwise AF and ANI values, we were able to ascertain mis-assignment of species names in genomes spanning nearly 18% of all existing species. Additionally, the complete linkage clustering made it possible to confidently assign species to nearly 326 genomes. Through the analysis of cliques, it has also become possible to identify speciation events within existing species. Within the JGI’s production pipeline, ANI is used to ascertain the species specificity of single cells and genomes extracted from metagenomes, and also as a metric for quality control within IMG. While ANI is integrated within IMG, ani.jgi.doe.gov serves the current data.

The mission of the Integrated Microbial Genomes & Microbiomes (IMG/M) system is to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at the JGI. IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M (see IMG/M submission site). The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available genome and metagenome datasets. IMG is a collaboration between the JGI and the Computational Biosciences Group at the Computing Sciences Research Division of LBNL.