SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis

BMC Bioinformatics. 2020 Aug 10;21(1):345. doi: 10.1186/s12859-020-03666-4.


Background: Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.

Results: Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at , and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at . Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis.

Conclusions: With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

Keywords: Differential analysis; Metagenomics; Visualization; Web application.

MeSH terms

  • Body Fluids / microbiology
  • Child, Preschool
  • Classification*
  • Feces / microbiology
  • Humans
  • Internet*
  • Metagenome
  • Metagenomics / methods*
  • Microbiota
  • RNA, Ribosomal, 16S / genetics
  • Software*
  • Statistics as Topic*
  • User-Computer Interface*
  • Workflow


  • RNA, Ribosomal, 16S