Phusion

Phusion assembles genome sequences from whole-genome shotgun (WGS) reads to generate high-quality draft assemblies for large, repeat-rich genomes.

Key Features:

• WGS assembly: Assembles genomes from whole-genome shotgun (WGS) sequencing reads.
• Repeat-rich genome handling: Designed to manage large and repeat-rich genomes such as the mouse.
• Read-pair integration: Leverages information on read pairs sharing common templates to inform assembly decisions.
• Preassembly clustering: Performs a preassembly stage that clusters reads into logical groups to improve accuracy.
• Cluster parallelization: Facilitates parallel processing by allowing each read cluster to be assembled independently.
• Scaffolded draft output: Produces scaffolded draft assemblies, exemplified by a ~2.6 gigabase mouse draft with ~90% of bases in 479 scaffolds at ~7.5x coverage.
• Cross-species performance: Demonstrated assembly of Caenorhabditis briggsae at approximately 11x coverage.

Scientific Applications:

• Mouse genome assembly: Generation of a high-quality draft assembly of the mouse genome (~2.6 Gb, ~7.5x coverage, 479 scaffolds covering ~90% of bases).
• Caenorhabditis briggsae assembly: Assembly of the C. briggsae genome at approximately 11x coverage.
• Comparative genomics: Enabling comparative analyses between species such as mouse and human through draft genome assemblies.
• Pathogen genomics and target identification: Supporting genomic studies of metazoan pathogens including Schistosoma mansoni and Schistosoma japonicum to inform identification of drug targets and interventions.

Methodology:

Phusion uses sequence reads and read-pair template information, performs a preassembly clustering of reads into logical groups, and assembles each cluster independently to enable parallelization.