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

  • Author(s): Chen, IMA
  • Chu, K
  • Palaniappan, K
  • Pillay, M
  • Ratner, A
  • Huang, J
  • Huntemann, M
  • Varghese, N
  • White, JR
  • Seshadri, R
  • Smirnova, T
  • Kirton, E
  • Jungbluth, SP
  • Woyke, T
  • Eloe-Fadrosh, EA
  • Ivanova, NN
  • Kyrpides, NC
  • et al.
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.

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