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Bioinformatics. 2014 Oct;30(19):2717-22. doi: 10.1093/bioinformatics/btu395. Epub 2014 Jun 19.

Omega: an overlap-graph de novo assembler for metagenomics.

Author information

1
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.

Abstract

MOTIVATION:

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.

AVAILABILITY AND IMPLEMENTATION:

Implemented in C++ with source code and binaries freely available at http://omega.omicsbio.org.

PMID:
24947750
DOI:
10.1093/bioinformatics/btu395
[Indexed for MEDLINE]

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