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FANTOM: Functional and taxonomic analysis of metagenomes

Kemal Sanli12, Fredrik H Karlsson1, Intawat Nookaew1* and Jens Nielsen1*

Author Affiliations

1 Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, SE 412 96, Sweden

2 Present Address: Department of Biological and Environmental Sciences, University of Gothenburg, Box 100, Gothenburg, S-405 30, Sweden

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BMC Bioinformatics 2013, 14:38  doi:10.1186/1471-2105-14-38

Published: 1 February 2013



Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context.


Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases.


The software is implemented in Python, is platform independent, and is available at webcite

Graphical User Interface (GUI); Metagenomics; Statistical analysis; Multivariate analysis; Visualization