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

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.
 [1] ;  [1] ;  [2] ;  [1] ;  [2] ;  [1]
  1. ORNL
  2. U.S. Department of Energy, Joint Genome Institute
Publication Date:
OSTI Identifier:
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Bioinformatics; Journal Volume: 30; Journal Issue: 19
Research Org:
Oak Ridge National Laboratory (ORNL); Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org:
ORNL work for others; ORNL LDRD Director's R&D
Country of Publication:
United States