FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Jiwoong Kim, Min Soo Kim, Andrew Koh, Yang Xie, Xiaowei Zhan

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Background: Given the lack of a complete and comprehensive library of microbial reference genomes, determining the functional profile of diverse microbial communities is challenging. The available functional analysis pipelines lack several key features: (i) an integrated alignment tool, (ii) operon-level analysis, and (iii) the ability to process large datasets. Results: Here we introduce our open-sourced, stand-alone functional analysis pipeline for analyzing whole metagenomic and metatranscriptomic sequencing data, FMAP (Functional Mapping and Analysis Pipeline). FMAP performs alignment, gene family abundance calculations, and statistical analysis (three levels of analyses are provided: differentially-abundant genes, operons and pathways). The resulting output can be easily visualized with heatmaps and functional pathway diagrams. FMAP functional predictions are consistent with currently available functional analysis pipelines. Conclusion: FMAP is a comprehensive tool for providing functional analysis of metagenomic/metatranscriptomic sequencing data. With the added features of integrated alignment, operon-level analysis, and the ability to process large datasets, FMAP will be a valuable addition to the currently available functional analysis toolbox. We believe that this software will be of great value to the wider biology and bioinformatics communities.

Original languageEnglish (US)
Article number420
JournalBMC Bioinformatics
Volume17
Issue number1
DOIs
StatePublished - Oct 10 2016

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Metagenomics
Operon
Functional analysis
Pipelines
Functional Analysis
Microbial Genome
Computational Biology
Genes
Alignment
Software
Large Data Sets
Sequencing
Pathway
Gene
Functional Data
Bioinformatics
Biology
Statistical Analysis
Statistical methods
Genome

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

FMAP : Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies. / Kim, Jiwoong; Kim, Min Soo; Koh, Andrew; Xie, Yang; Zhan, Xiaowei.

In: BMC Bioinformatics, Vol. 17, No. 1, 420, 10.10.2016.

Research output: Contribution to journalArticle

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