IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

By I-Min A. Chen, Ken Chu, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, Marcel Huntemann, Neha J. Varghese, James Robert White, Rekha Seshadri and 7 more. Nucleic Acids Res., 2018

759 citations recorded by the source corpus.

Abstract The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE’s Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG’s web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) allows registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has grown by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b58e98029d53d69ccc7089dca7b01bf050b5ad2b

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Citations in the corpus

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).”
MGnify: the microbiome analysis resource in 2020 (2019, background): “Indeed, a similar conclusion has been drawn by the IMG / M resource (22), who are currently backfilling old assemblies that used an alternative approach with metaSPAdes derived assemblies.”
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, methodology): “(i) 2 028 310 sequences were obtained by mining public IMG/M (21) metagenomes (up to 15 December 2019) using the Earth’s Virome protocol (31), which includes a minimum contig size of 5 kb (hereafter ‘EVP’).”
Deep learning-based prediction of protein structure using learned representations of multiple sequence alignments (2020, methodology): “MSAs were built using an approach similar to that taken by our group in CASP13 [5] , using the UniClust30 2020_03 database, plus protein sequences from the UniRef100 [17] , EBI MGnify [18] , IMG/M [19] , MetaEuk [20] , and NCBI Transcriptome Shotgun Assembly databases.”
A genomic catalog of Earth’s microbiomes (2020, methodology): “Custom species and gene trees for mcrABG-encoding Archaea The 15 archaeal GEMs which encoded for the mcrABG operon were added to a representative set of 652 publicly available archaeal genomes downloaded from the Integrated Microbial Genomes and Microbiomes (IMG/M) online database [11] (database acc”