Metagenome-wide association studies software tools | Shotgun metagenomic sequencing data analysis
Metagenome-wide association studies (MWAS) have enabled the high-resolution investigation of associations between the human microbiome and several complex diseases, including type 2 diabetes, obesity, liver cirrhosis, colorectal cancer and rheumatoid arthritis. The associations that can be identified by MWAS are not limited to the identification of taxa that are more or less abundant, as is the case with taxonomic approaches, but additionally include the identification of microbial functions that are enriched or depleted.
Leverages pre-existing databases, annotations and frameworks, along with manual curation. BugBase is an algorithm with a user-friendly graphical user interface (GUI) for analyzing microbiome data developed to provide users with biologically relevant microbiome phenotype predictions at the organism level. This method is also unable to model and predict cell-to-cell heterogeneity within strains due to genetic mutations and horizontal gene transfer. BugBase is available as a desktop app and as a web app.
Determines underlying microbial community structures and associations between microbiota and their environmental factors from microbial metagenome data. ENIGMA is a hierarchical Bayesian model based on a probabilistic model of a microbial community structures. The software can be used to learn how enterotype-like clusters of operational taxonomic units (OTUs) contribute to microbial structure and how microbial compositional patterns might be related to the known features of the sample. Moreover, this method was applied to clinical metagenomics data.
Characterizes microbial samples from nucleotide or protein sequences. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities. The software suggests protein families associated with the presence of particular phenotypes. It may help researchers in microbiology to pinpoint the traits of interest, reducing the amount of wet lab work required.
Offers a method for visualizing multi-omics biological studies. VOLARE is an application composed of two main parts: (i) a set of R scripts for pairwise regressions calculations and; (ii) a web platform supplying features including a mean to generate plots of interest, network and a top table that can be combined. It allows the visualization of the results of individual microbiome and immune cell assays, regressions, and as well as biological networks.
Allows users to test the mediation effect of the human microbiome. MedTest is a program assisting researchers to detect the structured mediators and can be applied to any genomics data with different structures (e.g., linkage disequilibrium (LD) structure for genetic data). It focuses on identifying mediation effect by using an ensemble of distance measures and can recognize specific taxa or operational taxonomic units (OTUs) accounting for the mediation effect.
Investigates links between a specific disease and microbiota. BERMUDA is a package intending to consider individual differences in a given microbial composition to detect combinations of taxa that can be regarded as characteristic of a specific disease risk. This program leans on a probabilistic model which is merged to a learning procedure that uses an annealing expectation maximization (EM) algorithm.
Provides a method for studying population-scale microbiome. tmap enables the adoption of topological data analysis (TDA) in microbiome data analysis pipelines, thus permitting users to interpret large-scale complex data. It also offers a network-based statistical method for enterotype analysis, driver species identification, and microbiome-wide association of host meta-data.