SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Summary: Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

Original languageEnglish
Pages (from-to)354-361
Number of pages8
JournalBioinformatics
Volume32
Issue number3
DOIs
Publication statusPublished - 1 Feb 2016
Externally publishedYes

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords

  • metagenomics
  • Microbial communities
  • Data analysis
  • SUPER-FOCUS

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