IMG/M: integrated genome and metagenome comparative data analysis system

By I-Min A. Chen, Victor M. Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann and 6 more. 2016

421 citations recorded by the source corpus.

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review (ER) companion system (IMG/M ER: https://img.jgi.doe.gov/mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes (2018, background): “Most of the UI layout remains the same as described in the previous IMG publications (27).”
Genomes OnLine Database (GOLD) v.8: overview and updates (2020, background): “Well-defined genome and metagenome projects in GOLD are a prerequisite for sub-mitting sequence data to the Integrated Microbial Genomes with Microbiome (IMG / M) (17) system for annotation and analysis (18,19).”
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, background): “Existing automated pipelines and cloud services lack modularity, do not give users control over the analysis, and often lack functions for genome-resolved metagenomics, the extraction of putative genomes (bins) through the binning of metagenomic assemblies [14, 16-19].”