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Title: Omega: an Overlap-graph de novo Assembler for Meta-genomics

Abstract

Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.

Authors:
 [1];  [1];  [2];  [1];  [2];  [1]
  1. ORNL
  2. U.S. Department of Energy, Joint Genome Institute
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC); Work for Others (WFO); USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1158737
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 30; Journal Issue: 19; Journal ID: ISSN 1367-4803
Country of Publication:
United States
Language:
English

Citation Formats

Haider, Bahlul, Ahn, Tae-Hyuk, Bushnell, Brian, Chai, JJ, Copeland, Alex, and Pan, Chongle. Omega: an Overlap-graph de novo Assembler for Meta-genomics. United States: N. p., 2014. Web. doi:10.1093/bioinformatics/btu395.
Haider, Bahlul, Ahn, Tae-Hyuk, Bushnell, Brian, Chai, JJ, Copeland, Alex, & Pan, Chongle. Omega: an Overlap-graph de novo Assembler for Meta-genomics. United States. doi:10.1093/bioinformatics/btu395.
Haider, Bahlul, Ahn, Tae-Hyuk, Bushnell, Brian, Chai, JJ, Copeland, Alex, and Pan, Chongle. Wed . "Omega: an Overlap-graph de novo Assembler for Meta-genomics". United States. doi:10.1093/bioinformatics/btu395.
@article{osti_1158737,
title = {Omega: an Overlap-graph de novo Assembler for Meta-genomics},
author = {Haider, Bahlul and Ahn, Tae-Hyuk and Bushnell, Brian and Chai, JJ and Copeland, Alex and Pan, Chongle},
abstractNote = {Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.},
doi = {10.1093/bioinformatics/btu395},
journal = {Bioinformatics},
issn = {1367-4803},
number = 19,
volume = 30,
place = {United States},
year = {2014},
month = {1}
}

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