HUBDesign

HUBDesign generates probe sets using sequence homology to enrich multiple metagenomic targets across taxonomic levels for targeted metagenomic sequencing and pathogen detection.

Key Features:

• Simultaneous Target Capture: Designs probes capable of capturing a wide array of metagenomic targets concurrently to enable enrichment of multiple organisms in a single assay.
• Balanced Probe Design: Balances probe depth and breadth to provide comprehensive coverage while maintaining target specificity.
• Taxonomic Flexibility: Enables probe design at multiple taxonomic levels to target species, strains, or broader taxonomic groups.
• Sequence Homology-Based Probe Construction: Leverages sequence homology to construct probes that target known sequences and related variants.
• Experimental Validation Evidence: Demonstrated simultaneous enrichment of coronaviruses (including SARS-CoV-2 and HCoV-NL63 from a human RNA background) and capture of seven bacterial strains from human blood in sepsis-related studies.

Scientific Applications:

• Viral Pathogen Detection: Enrichment and detection of diverse coronaviruses including SARS-CoV-2 and HCoV-NL63 from complex human RNA backgrounds.
• Bacterial Pathogen Enrichment: Targeted enrichment of bacterial pathogens, demonstrated by capture of seven strains from human blood in sepsis-associated samples.
• Metagenomic Target Enrichment: Enriches diverse metagenomic targets to improve sensitivity for pathogen detection and microbial diversity studies in complex biological samples.

Methodology:

Uses sequence homology to design probes that balance specificity and breadth, constructing probe sets that target known sequences and related variants while optimizing probe depth and coverage.