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

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:
 [1] ;  [2] ;  [3] ;  [4]
  1. San Diego State Univ. San Diego, CA (United States). Computational Science Research Center
  2. San Diego State Univ. San Diego, CA (United States). Dept. of Biology
  3. Univ. of Utrecht (Netherlands); Radboud Univ., Nijmegen (Netherlands); Federal Univ. of Rio de Janeiro (Brazil)
  4. 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:
OSTI Identifier:
1261146
Grant/Contract Number:
CNS-1305112; MCB-1330800; DUE-132809
Type:
Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 32; Journal Issue: 3; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Research Org:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org:
USDOE; National Science Foundation (NSF)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES