The Integrated Microbial Genomes (IMG) system provides tools for analyzing the structural and functional annotations of metagenomes and single genomes in a comparative context. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets (sets of genome sequence fragments from microbial communities) sequenced at the DOE Joint Genome Institute (JGI) or provided directly by scientists, as well as public bacterial, archaeal, eukaryotic, and viral genomes from the US National Center for Biotechnology Information (NCBI) The metagenome datasets included in IMG also encompass a rich set of metagenomes from engineered, environmental and host associated communities. Genomes and metagenome datasets from JGI, as well as those provided by outside scientists, are included in IMG after they are processed using IMG’s microbial genome and metagenome sequence data processing pipelines. Genomes from NCBI are included into IMG with their native structural and functional annotations.
Starting Dec 1st, 2014, genomes from NCBI will be processed using IMG’s data processing pipelines before they are included into IMG. This change of data processing policy aims at improving the breadth, depth and consistency of structural and functional annotation across all genomes in IMG. The new policy complies with the results of a collaborative effort conducted by JGI, NCBI, JCVI, Broad and IGS scientists in evaluating the accuracy of different gene calling pipelines. The conclusion of this evaluation (described in a paper submitted for publication) is that while yielding slightly different results, gene calling pipelines are comparable in accuracy and therefore comparative analyses will benefit from using the same pipeline for annotating genomes included in a system such as JGI’s IMG or NCBI’s RefSeq.
Since IMG provides individual annotated genome datasets processed using its pipelines through JGI’s genome portals, all genomes from NCBI will be also available through these portals.