IMG/M: a data management and analysis system for metagenomes

By Victor M. Markowitz, Natalia N. Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Y. Grechkin, I-Min A. Dubchak, Iain Anderson and 4 more. Nucleic Acids Res., 2007

377 citations recorded by the source corpus.

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9bd549a9d8550a0ef633eab55573639bf7fb3174

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Citations in the corpus

Chapter 12: Human Microbiome Analysis (2012, methodology): “Computational tools for metagenomic analysis include [13,19,63,75,76,77,166].”
A Primer on Metagenomics (2010, methodology): “MG-RAST provides a comparative functional and sequence-based analysis for uploaded samples, whereas IMG/M provides similar analysis for metagenomes that exist in the IMG/M site [105].”
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata (2011, methodology): “For that purpose, the GOLD metadata are integrated into the Integrated Microbial Genomes (IMG) family of data management systems (11–13).”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “…have been developed to determine the functional attributes in shotgun metagenomics data, including MG-RAST (Meyer et al., 2008), MEGAN (Mitra et al., 2011), IMG/M (Markowitz et al., 2008), HUMAnN (Abubucker et al., 2012), and the R package ShotgunFunctionalizeR (Kristiansson et al., 2009).”
Ultrafast clustering algorithms for metagenomic sequence analysis (2012, methodology): “Both MG-RAST [45] and IMG/M [46] use prefix checking for identification of duplicates.”
The MG-RAST metagenomics database and portal in 2015 (2015, methodology): “The DOE Joint Genome Institute’s IMG/M (22) pipeline now requires data to be created by JGI (personal communication, Nikos Kyrpides, JGI).”
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource (2010, background): “(iii) Data exchange with public data resources like NCBI (5), IMG/M (6) and MG-RAST (7).”
Ab initio gene identification in metagenomic sequences (2010, methodology): “Metagenomic sequence data and annotation for human and mouse gut microbiomes were from the JGI IMG/M database (24).”
Metagenomics - a guide from sampling to data analysis (2012, methodology): “MG-RAST, IMG/M, and CAMERA are three prominent systems [43,50,74].”
Manipulating the soil microbiome to increase soil health and plant fertility (2012, methodology): “Yet, recent studies using six publicly available rhizosphere microbiomes (Markowitz et al. 2008) were used to analyze the functional content of the assembled and unassembled reads from rhizosphere and bulk soil (Barret et al. 2011).”