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

doi:10.1093/bioinformatics/btv584

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 journal › Article › peer-review

124 Citations (Scopus)

54 Downloads (Pure)

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 language	English
Pages (from-to)	354-361
Number of pages	8
Journal	Bioinformatics
Volume	32
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btv584
Publication status	Published - 1 Feb 2016
Externally published	Yes

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

Access to Document

10.1093/bioinformatics/btv584Licence: CC BY

Silva_SUPER_P2016Final published version, 1.05 MBLicence: CC BY

Cite this

@article{f5ff1a3429ca44f4a896bdadb9b4c11b,

title = "SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data",

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.",

keywords = "metagenomics, Microbial communities, Data analysis, SUPER-FOCUS",

author = "Silva, {Genivaldo Gueiros Z.} and Green, {Kevin T.} and Dutilh, {Bas E.} and Edwards, {Robert A.}",

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.",

year = "2016",

month = feb,

day = "1",

doi = "10.1093/bioinformatics/btv584",

language = "English",

volume = "32",

pages = "354--361",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "3",

}

TY - JOUR

T1 - SUPER-FOCUS

T2 - A tool for agile functional analysis of shotgun metagenomic data

AU - Silva, Genivaldo Gueiros Z.

AU - Green, Kevin T.

AU - Dutilh, Bas E.

AU - Edwards, Robert A.

N1 - 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.

PY - 2016/2/1

Y1 - 2016/2/1

N2 - 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.

AB - 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.

KW - metagenomics

KW - Microbial communities

KW - Data analysis

KW - SUPER-FOCUS

UR - http://www.scopus.com/inward/record.url?scp=84962263095&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btv584

DO - 10.1093/bioinformatics/btv584

M3 - Article

C2 - 26454280

AN - SCOPUS:84962263095

SN - 1367-4803

VL - 32

SP - 354

EP - 361

JO - Bioinformatics

JF - Bioinformatics

IS - 3

ER -

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

Abstract

Bibliographical note

Keywords

Access to Document

Other files and links

Fingerprint

Cite this