title: SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS.
  
  
  BACKGROUND
  redwards@mail.sdsu.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Computational Science Research Center.
authors.forename: Genivaldo Gueiros Z
authors.initials: GG
authors.lastname: Silva
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA 92182, USA.
authors.forename: Kevin T
authors.initials: KT
authors.lastname: Green
authors.affiliation: Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6525 GA, Nijmegen, The Netherlands Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil.
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.affiliation: Computational Science Research Center Department of Biology, San Diego State University, San Diego, CA 92182, USA Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Brazil Department of Computer Science, San Diego State University, San Diego, CA 92182, USA Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, IL 60439, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
mesh_terms: D057894:Coral Reefs; D004247:DNA / Q000737:chemistry; D056186:Metagenomics / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D004247:DNA