IMG/M: Integrated Microbial Genomes & Microbiomes

IMG/M Mission top

The mission of the Integrated Microbial Genomes & Microbiomes(IMG/M) system is to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI).

IMG/M is also open to scientists worldwide for the annotation, analysis, and distribution of their own genome and microbiome datasets, as long as they agree with the IMG/M data release policy and follow the metadata requirements for integrating data into IMG/M (see IMG/M submission site).

IMG/M Access & Users top

IMG/M is committed to provide scientists worldwide free support for genome & microbiome data annotation & integration and open access comparative analysis of integrated genome and microbiome datasets.

IMG/M can be accessed without a login and password for searching and analyzing public datasets; dataset downloads, data exports and other advanced tools are provided via IMG/M ER which can be accessed with login/password.

IMG/M ER (Expert Review) users need to register at: JGI Single Sign On (JGI SSO) in order to obtain a login and password.
Logins/passwords allow users to:

  1. submit their own genomes/microbiome datasets and keep them "private" for up to two years while they review and revise annotations
  2. employ IMG/M's curation tools for identifying and correcting annotation anomalies, such as protein products, for both private or public genomes-annotation revisions are recorded/saved in user specific "MyIMG" files on IMG/M's file system
  3. employ IMG/M's Workspace which supports a persistent version of IMG/M's "Carts" and performing long running analysis computations;
  4. download IMG/M genome and microbiome datasets via JGI's Portals.

As of June 2016, IMG had over15,200 users from 89 countries across 6 continents. User Map

Data Distribution & Distribution Policy top

Microbial genome and microbiome datasets submitted for annotation and/or integration in IMG/M will be:

For datasets with multiple submissions, only the latest version will be kept in IMG/M, with older versions automatically removed.

Microbial genome and microbiome datasets submitted for annotation and/or integration in IMG/M are distributed solely through individual JGI data portals and are limited to assembled and annotated datasets; no other type of data distribution (data downloads) is provided. (Not all datasets are available for download because of various legal issues)

Microbial genomes sequenced at JGI become eligible for submission to Genbank when they become public in IMG/M. Genomes submitted by external users for annotation and comparative analysis in IMG/M are not submitted to Genbank by IMG/M. For such genomes Genbank submission is the responsibility of external users.

IMG/M Data Warehouse top

IMG/M's Data Warehouse integrates microbial genome and microbiome datasets sequenced at JGI or provided by IMG/M's users with a comprehensive set of publicly available bacterial, archaeal, eukaryotic, and phage genomes from Genbank, as well as engineered, environmental and host associated microbiome samples.

Added Microbial Genome and Microbiome Datasets
Year New Genomes New Metagenomes JGI Sequenced Genomes JGI Sequenced Metagenomes User Submitted Genomes User Submitted Metagenomes Genomes From Genbank
201310,1411,2652,385725 1,4045406,352
201413,9891,6682,309982 99668610,684
201511,4373,0772,6571,670 2,2351,4707,372

At the start of 2016, IMG/M had a total of 38,395 genome datasets from all domains of life and 8,077 microbiome datasets, out of which 33,116 genome datasets and 4,615 microbiome datasets are publicly available. Note that some genome and microbiome datasets have been deleted because of sequencing or annotation quality problems or have been replaced by newer versions.

Genes in IMG/M are characterized using several functional resources, including:

Through regular content updates, IMG/M aims at providing high levels of genome diversity, in terms of the number of genomes integrated into the system; annotation coverage, in terms of the breadth of the functional annotations; and data quality, in terms of the coherence of annotations. About 20% of the genomes and 75% of the metagenome samples in IMG/M were sequenced at DOE's Joint Genome Institute.

IMG/M Data Marts top

Microbial Genome and Microbiome Data Analysis
img IMG/M
IMG/M provides free access to public genome & microbiome datasets.
img mer IMG/M ER
IMG/M ER provides login access to private and public genome & microbiome datatsets, with support for data curation, dataset downloads and workspace analysis and data exports.
img abc IMG/ABC
IMG/ABC a knowledge base to fuel the discovery of biosynthetic gene clusters and novel secondary metabolites in IMG
img/vr IMG/VR (Viral)
The IMG/VR system serves as a starting point for the sequence analysis of viral fragments derived from metagenomic samples.
img/proportal IMG/ProPortal
BETA

IMG/M Other top

img submission Microbial Genome and Microbiome Data Set Submission
To submit your data sets for analysis in IMG/ER
IMG User Forum IMG User Forum
Where users can view documents, FAQ and ask questions.

IMG/M References top

Markowitz VM et al. (2014) IMG 4 version of the integrated microbial genomes comparative analysis system, Nucl. Acids Res. 42, D560-D567.
http://nar.oxfordjournals.org/content/42/D1/D560

Markowitz VM et al. (2014) IMG/M 4 version of the integrated metagenome comparative analysis system, Nucl. Acids Res. 42, D568-D573.
http://nar.oxfordjournals.org/content/42/D1/D568