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FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies.
Jiwoong Kim1,2, Min Soo Kim1,2, Andrew Y Koh2,3,4
1Department of Clinical Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA.
BMC Bioinformatics
|October 12, 2016
Summary
A new functional analysis pipeline, FMAP, addresses challenges in microbial community analysis. This tool integrates alignment, operon-level analysis, and large dataset processing for comprehensive metagenomic and metatranscriptomic data interpretation.
Area of Science:
- Bioinformatics
- Microbial Genomics
- Computational Biology
Background:
- Determining microbial community functional profiles is hindered by incomplete reference genomes.
- Existing functional analysis pipelines lack integrated alignment, operon-level analysis, and large dataset processing capabilities.
Purpose of the Study:
- Introduce FMAP (Functional Mapping and Analysis Pipeline), an open-sourced, stand-alone tool for analyzing metagenomic and metatranscriptomic sequencing data.
- Provide a comprehensive solution for microbial community functional profiling.
Main Methods:
- FMAP integrates alignment, gene family abundance calculations, and statistical analysis.
- Supports analysis at gene, operon, and pathway levels.
- Enables visualization of results using heatmaps and functional pathway diagrams.
Main Results:
- FMAP successfully performs alignment, abundance calculations, and statistical analyses.
- The pipeline provides functional predictions consistent with existing tools.
- Output is easily visualized, facilitating interpretation of complex datasets.
Conclusions:
- FMAP offers a comprehensive functional analysis tool for metagenomic and metatranscriptomic data.
- Its integrated alignment, operon-level analysis, and large dataset capabilities enhance current bioinformatics toolboxes.
- FMAP is expected to be valuable for the biology and bioinformatics communities.
