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

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/) enabled 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 increased 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.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Resphera Biosciences, Baltimore, MD (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Energy Research Scientific Computing Center (NERSC)
OSTI Identifier:
1542357
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 47; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States: N. p., 2018. Web. doi:10.1093/nar/gky901.
Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., & Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States. doi:10.1093/nar/gky901.
Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. Fri . "IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes". United States. doi:10.1093/nar/gky901. https://www.osti.gov/servlets/purl/1542357.
@article{osti_1542357,
title = {IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes},
author = {Chen, I-Min A. and Chu, Ken and Palaniappan, Krishna and Pillay, Manoj and Ratner, Anna and Huang, Jinghua and Huntemann, Marcel and Varghese, Neha and White, James R. and Seshadri, Rekha and Smirnova, Tatyana and Kirton, Edward and Jungbluth, Sean P. and Woyke, Tanja and Eloe-Fadrosh, Emiley A. and Ivanova, Natalia N. and Kyrpides, Nikos C.},
abstractNote = {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/) enabled 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 increased 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.},
doi = {10.1093/nar/gky901},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United States},
year = {2018},
month = {10}
}

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    Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species
    journal, May 2019

    • Syed, Puleng Rosinah; Chen, Wanping; Nelson, David R.
    • International Journal of Molecular Sciences, Vol. 20, Issue 11
    • DOI: 10.3390/ijms20112690

    Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
    journal, October 2019

    • Ambrosino, Luca; Tangherlini, Michael; Colantuono, Chiara
    • Marine Drugs, Vol. 17, Issue 10
    • DOI: 10.3390/md17100576

    Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA
    journal, April 2019


    Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs)
    journal, January 2020

    • Coffinet, Sarah; Meador, Travis B.; Mühlena, Lukas
    • Biogeosciences, Vol. 17, Issue 2
    • DOI: 10.5194/bg-17-317-2020

    Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
    journal, April 2019


    MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
    journal, January 2019