title: Omega: an overlap-graph de novo assembler for metagenomics.
abstract: BACKGROUND
  Metagenomic sequencing allows reconstruction of microbial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed 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 short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information. In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.
  
  
  METHODS
  Implemented in C++ with source code and binaries freely available at http://omega.omicsbio.org.
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Bahlul
authors.initials: B
authors.lastname: Haider
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Tae-Hyuk
authors.initials: TH
authors.lastname: Ahn
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Bushnell
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Chai
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Copeland
authors.affiliation: Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 and U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598 USA.
authors.forename: Chongle
authors.initials: C
authors.lastname: Pan
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D004269:DNA, Bacterial / Q000032:analysis*; D016680:Genome, Bacterial; D020407:Internet; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004269:DNA, Bacterial