RAMBO-K

RAMBO-K assigns reads from mixed NGS datasets to their originating organisms using k-mer signatures to separate viral and endosymbiont sequences from host reads for downstream genome assembly.

Key Features:

• Rapid and sensitive read separation: Removes host sequences from mixed NGS datasets to enrich target viral or endosymbiont reads with high sensitivity and specificity.
• K-mer-based classification: Uses k-mer signatures and focuses on unique k-mers to distinguish host and non-host sequences.
• High-throughput performance: Processes data at 10 Megabases per second using four CPU cores and a standard hard drive.
• No input preprocessing required: Separates reads from different species without prior data preprocessing.

Scientific Applications:

• Viral genome assembly: Enriches viral reads from host-dominated NGS datasets to facilitate viral genome reconstruction.
• Endosymbiont genome assembly: Separates endosymbiont reads from host sequences to support endosymbiont genome assembly.
• Host versus non-host read separation: Filters host reads in mixed NGS datasets to improve downstream genomic analyses.

Methodology:

Assigns reads to organisms using a k-mer-based approach that focuses on unique k-mers to distinguish host and non-host sequences.