Microbiome Analysis Toolbox

The Microbiome Analysis Toolbox is a comprehensive online platform designed to support researchers in their microbiome research. Developed at the European Molecular Biology Laboratory (EMBL), this toolbox provides a suite of tools and resources for analyzing and interpreting microbiome data such as identification and quantification of microorganisms, working with cellular pathways, phylogenetic trees and microbial communities.

Key Features:
  • Modular Tools: The toolbox offers a range of modular tools, each addressing specific steps in the microbiome analysis workflow, including data preprocessing, taxonomic classification, functional profiling, and statistical analysis.
  • Easy-to-Use Interface: Users can access these tools through an intuitive web interface, making it easy to analyze microbiome data without requiring extensive bioinformatic expertise.
  • Customizable Workflows: The toolbox allows users to create custom workflows by combining individual tools in a flexible and modular way.
  • Streamlined Analysis: The Microbiome Analysis Toolbox streamlines the analysis of microbiome data, saving researchers time and effort.
Tools:

mOTUs

  • Quantifies known and unknown microorganisms at species-level resolution from shotgun sequencing data
  • Clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs
  • Profiles abundances of mOTUs in shotgun metagenomic samples
  • Enables identification of novel microorganisms not previously represented in databases

eggNOG

  • Provides orthologous group assignments at over 100 different taxonomic levels
  • Offers multiple sequence alignments, maximum-likelihood trees, and broad functional annotations for each group
  • Includes comprehensive characterization and analysis of gene families from over 2,000 complete genomes
  • Enables users to explore and analyze the evolution of gene functions across different organisms

iPATH

  • Visualizes and analyzes cellular pathways based on current annotations (such as KEGG)
  • Provides pathway maps for primary cellular metabolism and secondary metabolite synthesis and regulatory pathways
  • Allows users to map their own data onto these pathway maps
  • Enables easy exploration and analysis of the functional and metabolic capabilities of (meta-)genomic data sets

iTOL

  • Displays and manipulates phylogenetic trees in a variety of layouts, including circular tree layout
  • Offers drawing and annotation features for tree displays
  • Exports tree displays in several graphical formats, both bitmap and vector based
  • Enables users to easily visualize and analyze large phylogenetic datasets

Enterotyping

  • Detects and characterizes densely populated regions (enterotypes) in high-dimensional space of microbiome community composition
  • Stratifies human individuals by enterotype
  • Provides computational methods for detecting and characterizing enterotypes in any dataset
  • Enables researchers to reproduce previous reports or determine enterotypes in new studies

SIAMCAT

  • Performs statistical inference of associations between microbial communities and host phenotypes (such as disease states)
  • Uses LASSO models to avoid overfitting issues and enable model interpretation and biomarker selection
  • Offers a modular framework for integrating multiple data types and analysis methods
  • Enables identification of potential microbial biomarkers for diseases or other conditions

proGenomes

  • Provides consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes
  • Enables interactive exploration and download of subsets of the database (e.g., by taxonomic clade or habitat)
  • Offers customization options for subsets of organisms (e.g., representatives of each species or habitat-specific organisms)
  • Facilitates research on microbial ecology and evolution

NGLess

  • Provides a domain-specific language for next-generation sequencing data processing with a focus on metagenomics
  • Implements the NG-meta-profiler workflow, which efficiently and reproducibly performs sequence preprocessing, mapping to reference databases, filtering of the mapping results, and profiling
  • Offers flexible and customizable workflows for analyzing metagenomic data
  • Enables researchers to easily integrate NGLess into their existing bioinformatics pipelines

If you use a tool of the Toolbox please take the time to answer our short survey to help us improve our services: https://www.surveymonkey.de/r/denbi-service?sc=hd-hub&tool=microbiomeanalysistoolbox

Website
This email address is being protected from spambots. You need JavaScript enabled to view it.