Abstract
BackgroundInterpretation 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.ResultsHere 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.ConclusionsThe software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.
Highlights
Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples
For whole genome based metagenomics, extracted DNA from an environmental sample is a starting material to generate short reads of DNA through generation sequencing (NGS) technologies that represent the microbiota of the sample
We identified the requirement for a user-friendly comparative analysis and data visualization tool where annotated metagenomics data can meet sample metadata and be analyzed at different hierarchy levels using a built-in or user provided biological database
Summary
We introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. 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
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