The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

By Folker Meyer, Daniel Paarmann, M. D'Souza, R. Olson, Elizabeth M. Glass, Michael Kubal, Tobias Paczian, Alexis A. Rodriguez, Rick L. Stevens, Andreas Wilke and 2 more. 2008

3,462 citations recorded by the source corpus.

AbstractBackgroundRandom community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers.ResultsA high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. Phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standard views. User access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing datasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats.ConclusionThe open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis – the availability of high-performance computing for annotating the data. http://metagenomics.nmpdr.org

Subfields: Ecology, Molecular Biology

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Citations in the corpus

PhyloSift: phylogenetic analysis of genomes and metagenomes (2014, methodology): “Among the uses of phylogenetic analysis in metagenomics are: improved classification 68 of sequences using phylogenetic methods, functional prediction for genes, alternative metrics of alpha 69 and beta diversity, improved identification of operational taxonomic units (OTUs), and sequence binning 70”
Responses of Gut Microbiota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice (2011, background): “The sequences (68,163 reads) are publicly available at the MG-RAST repository (31) under ID 4449917.”
Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples (2009, methodology): “Shotgun data can be functionally or taxonomically classified using MEGAN [13], CARMA [32], or MG-RAST [33].”
454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. (2013, methodology): “, 2011) were detected in our samples by a search in MG-RAST (Meyer et al., 2008) and Silva SSU database (Pruesse et al.”
Metagenomic biomarker discovery and explanation (2011, methodology): “UniFrac [38] compares sets of metagenomes at a strictly taxonomic level using phylogenetic distance, while MGRAST [39], ShotgunFunctionalizeR [40], mothur [41], and METAREP [42] all process metagenomic data using standard statistical tests (mainly t-tests with some modifications).”
Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions (2013, methodology): “MG-RAST [36] and Mothur [37] were used for quality screening and sequence processing for each of the 5 samples.”