Seqwin

Seqwin automates the discovery of microbial genome signature sequences for sensitive and accurate pathogen detection by leveraging weighted pan-genome minimizer graphs and a traversal algorithm.

Key Features:

• Weighted pan-genome minimizer graphs: Seqwin builds weighted pan-genome minimizer graphs to represent large microbial genome collections.
• Traversal algorithm: Seqwin uses a traversal algorithm to identify signature sequences that occur frequently in target genomes but remain rare in non-targets.
• Variation accommodation: Seqwin accommodates natural sequence variation rather than depending on strict presence or absence of sequences.
• Scalability: Seqwin scales to very large genome collections, such as nearly 15,000 S. enterica genomes.
• Computational efficiency: Seqwin recovers more high-quality signatures than alternative methods with lower computational burden.

Scientific Applications:

• Pathogen detection: Seqwin enables robust pathogen detection for clinical, environmental, and public health applications.
• Diagnostic assay design: Seqwin provides a solution for scalable microbial signature discovery to support PCR-based diagnostic assay design.
• Species-specific signature identification: Seqwin identifies signatures for target microbial groups such as C. difficile, M. tuberculosis, and S. enterica.

Methodology:

Seqwin builds weighted pan-genome minimizer graphs and uses a traversal algorithm to identify signature sequences that occur frequently in target genomes but remain rare in non-targets.