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. 2019 Jan 8;47(D1):D666-D677.
doi: 10.1093/nar/gky901.

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

I-Min A Chen  1 , Ken Chu  1 , Krishna Palaniappan  1 , Manoj Pillay  1 , Anna Ratner  1 , Jinghua Huang  1 , Marcel Huntemann  1 , Neha Varghese  1 , James R White  2 , Rekha Seshadri  1 , Tatyana Smirnova  1 , Edward Kirton  1 , Sean P Jungbluth  1 , Tanja Woyke  1 , Emiley A Eloe-Fadrosh  1 , Natalia N Ivanova  1 , Nikos C Kyrpides  1
Affiliations

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

I-Min A Chen et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
IMG & GOLD Citation Overview. (i) IMG & GOLD Citation Overview page shows all papers citing IMG or GOLD. Publications are divided into different categories. (ii) Users can click on the category to see a set of papers in this category. The list can be searched or sorted. The example shows searching on ‘nucleic acids research’ (case insensitive) from the Search field at the right upper corner. (iii) Clicking on a title will lead to the actual publication.
Figure 2.
Figure 2.
Quick Search option for the new Genome Search feature. (i) The Quick Search option allows users to type in a keyword to search all IMG genomes. (ii) The search results can be added to Genome Cart.
Figure 3.
Figure 3.
Example application of the Advanced Search Builder option of the new Genome Search feature. (i) Users can build a complex query to find all soil metagenome datasets sampled at depth of up to 10 cm in Wisconsin or Michigan that are not classified as agricultural soils. (ii) Users can click the Evaluate Query button to see statistics information. (iii) Query result is displayed after the Search button is clicked.
Figure 4.
Figure 4.
Search History of the new Genome Search feature. (i) All searches done in a session will be saved. Users can also reconstruct and search any of the selected queries. (ii) Expert Review users have the additional ability to save any queries into the Workspace.
Figure 5.
Figure 5.
Decision tree for selection of default statistical test method. FDR is false discovery rate.
Figure 6.
Figure 6.
The new analysis tools are available in the Statistical Analysis tab of Workspace Genome Sets. In this particular example, the user selects two genome sets to measure gene count by Pfam using default system recommendation. Users can gather more information regarding analysis methods by clicking on the question mark to view a detailed description. The analysis will be run on the background and the result will be saved as a new job. The user can click on the Run Analysis button to submit the analysis request. UI will inform the user which default analysis method has been chosen.
Figure 7.
Figure 7.
Analysis statuses and results are available from My Jobs in Workspace. A job starts with waiting status. Users will be able to view the analysis result when a job is complete. The result data table can be exported. Users can also select to download a complete report.
Figure 8.
Figure 8.
New metagenome bins in IMG. (i) Metagenome Statistics in the metagenome detail page shows the number of bins. (ii) Users can view more detailed information of bins by clicking on the count. Expert Review users can also select one or more bins to save as workspace scaffold sets. (iii) After the user clicks the scaffold count, a new Metagenome Bin Scaffolds page will show up listing all scaffolds in the bin together with more detailed information on each scaffold.
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