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

Journal Article · · Bioinformatics
 [1];  [1];  [2];  [1];  [2];  [1]
  1. ORNL
  2. U.S. Department of Energy, Joint Genome Institute
+ Show Author Affiliations

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.

Research Organization:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Organization:
USDOE Office of Science (SC); Work for Others (WFO); USDOE Laboratory Directed Research and Development (LDRD) Program
DOE Contract Number:
DE-AC05-00OR22725
OSTI ID:
1158737
Journal Information:
Bioinformatics, Vol. 30, Issue 19; ISSN 1367-4803
Country of Publication:
United States
Language:
English

References (16)

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Bambus 2: scaffolding metagenomes journal September 2011
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Fast and accurate long-read alignment with Burrows–Wheeler transform journal January 2010
De novo assembly of human genomes with massively parallel short read sequencing journal December 2009
A Whole-Genome Assembly of Drosophila journal March 2000
The fragment assembly string graph journal September 2005
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads journal July 2012
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth journal April 2012
MetaSim—A Sequencing Simulator for Genomics and Metagenomics journal October 2008
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities: Metagenomic and rRNA diversity characterization journal February 2013
Efficient de novo assembly of large genomes using compressed data structures journal December 2011
ABySS: A parallel assembler for short read sequence data journal February 2009
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline journal January 2013
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008

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