SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
Abstract
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. We tested SUPER-FOCUS 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.
- Authors:
-
- San Diego State Univ. San Diego, CA (United States). Computational Science Research Center
- San Diego State Univ. San Diego, CA (United States). Dept. of Biology
- Univ. of Utrecht (Netherlands); Radboud Univ., Nijmegen (Netherlands); Federal Univ. of Rio de Janeiro (Brazil)
- San Diego State Univ. San Diego, CA (United States). Computational Science Research Center; San Diego State Univ. San Diego, CA (United States). Dept. of Biology; Federal Univ. of Rio de Janeiro (Brazil); San Diego State Univ. San Diego, CA (United States). Dept. of of Computer Science; Argonne National Lab. (ANL), Argonne, IL (United States)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE; National Science Foundation (NSF)
- OSTI Identifier:
- 1261146
- Grant/Contract Number:
- CNS-1305112; MCB-1330800; DUE-132809
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Bioinformatics
- Additional Journal Information:
- Journal Volume: 32; Journal Issue: 3; Journal ID: ISSN 1367-4803
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Silva, Genivaldo Gueiros Z., Green, Kevin T., Dutilh, Bas E., and Edwards, Robert A. SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. United States: N. p., 2015.
Web. doi:10.1093/bioinformatics/btv584.
Silva, Genivaldo Gueiros Z., Green, Kevin T., Dutilh, Bas E., & Edwards, Robert A. SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. United States. https://doi.org/10.1093/bioinformatics/btv584
Silva, Genivaldo Gueiros Z., Green, Kevin T., Dutilh, Bas E., and Edwards, Robert A. Fri .
"SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data". United States. https://doi.org/10.1093/bioinformatics/btv584. https://www.osti.gov/servlets/purl/1261146.
@article{osti_1261146,
title = {SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data},
author = {Silva, Genivaldo Gueiros Z. and Green, Kevin T. and Dutilh, Bas E. and Edwards, Robert A.},
abstractNote = {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. We tested SUPER-FOCUS 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.},
doi = {10.1093/bioinformatics/btv584},
journal = {Bioinformatics},
number = 3,
volume = 32,
place = {United States},
year = {Fri Oct 09 00:00:00 EDT 2015},
month = {Fri Oct 09 00:00:00 EDT 2015}
}
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