Dataset Information
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
Ontology highlight
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.Availability and implementation
SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS.Contact
redwards@mail.sdsu.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Silva GG
PROVIDER: S-EPMC4734042 | biostudies-literature | 2016 Feb
REPOSITORIES: biostudies-literature
Publications
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
Bioinformatics (Oxford, England) 20151009 3
<h4>Summary</h4>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 numbe ...[more]
