Ray

Ray: De novo genome and metagenome assembler

Ray performs de novo assembly of genomes and metagenomes using distributed parallel computing and integrates reads from multiple high-throughput sequencing technologies, including Roche/454 and Illumina, to improve assembly accuracy and reduce contig counts and platform-specific biases.

Key Features:

• Massively Distributed Metagenome Assembly: Ray Meta assembles large-scale metagenomic datasets using distributed computing, processing up to three billion reads representing 1,000 bacterial genomes in 15 hours with 1,024 processor cores and 1.5 GB memory per core.
• K-mer Coloring for Microbiome Profiling: Uses uniquely-colored k-mers to enable taxonomic profiling and abundance analysis of microbial communities.
• Multi-platform Read Integration: Combines sequencing reads from Roche/454 and Illumina to mitigate platform-specific biases and reduce assembly errors.

Scientific Applications:

• Metagenomic Research: Analyzes large environmental metagenomic datasets to characterize microbial diversity, composition, and function.
• Hybrid Genome Assembly: Produces high-quality genome assemblies from mixed sequencing technologies.

Methodology:

Ray applies distributed parallel computing to partition assembly workloads across multiple processor cores. It constructs assemblies using de Bruijn graph-based approaches with uniquely-colored k-mers for species discrimination and integrates reads from multiple sequencing platforms to reduce contig fragmentation and sequencing bias.