Omega

Omega assembles and scaffolds microbial genomes from Illumina sequencing data to reconstruct genomes directly from environmental microbial community samples.

Key Features:

• Overlap graph construction: constructs an overlap graph from sequencing reads.
• Overlap detection: identifies overlaps using a prefix/suffix hash table approach to capture potential sequence connections.
• Graph simplification: removes transitive edges and short branches to streamline the overlap graph.
• Unitig generation: generates unitigs via minimum cost flow analysis on the overlap graph representing contiguous sequences.
• Scaffolding: merges unitigs into contigs and scaffolds using mate-pair information for ordering and orientation.

Scientific Applications:

• Metagenomic assembly: assembles and scaffolds Illumina reads from microbial communities to reconstruct genomes from environmental samples.
• Performance on short reads: achieves comparable results to SOAPdenovo, IDBA-UD, and MetaVelvet on HiSeq 100-bp datasets.
• Performance on longer reads: outperforms SOAPdenovo, IDBA-UD, and MetaVelvet on MiSeq 300-bp datasets, indicating enhanced handling of longer reads.
• Comparison to OLC assemblers: produced more continuous assemblies and required less computing time than the Celera overlap-layout-consensus assembler on the MiSeq dataset.

Methodology:

Constructs an overlap graph from reads by identifying overlaps with a prefix/suffix hash table, removes transitive edges and short branches, generates unitigs via minimum cost flow analysis on the overlap graph, and merges unitigs into contigs and scaffolds using mate-pair information.