sourmash

sourmash computes compact MinHash sketches of DNA and RNA sequence collections to enable efficient comparison and search of genomic signatures using the Jaccard index.

Key Features:

• MinHash sketching: Computes compact MinHash sketches that represent large DNA or RNA sequence collections as signatures.
• Space-efficient storage: Stores genomic signatures in a space-efficient format via MinHash sketching.
• Jaccard-based comparison: Performs similarity comparisons and database searches using the Jaccard index between sketches.
• Sample identification and similarity search: Enables identification of samples and rapid retrieval of similar samples within large datasets by comparing signatures.
• Shared-sequence detection: Detects sequences shared across different datasets by measuring sketch overlap.
• Phylogenetic reconstruction: Supports construction of phylogenetic trees from sketch-based similarity measures.

Scientific Applications:

• Sample identification: Attributing DNA or RNA samples to known sources by comparing MinHash signatures.
• Similar-sample discovery: Finding similar DNA or RNA samples within large sequence collections using Jaccard similarity of sketches.
• Shared-sequence analysis: Identifying sequences shared between datasets through sketch overlap comparisons.
• Phylogenetic analysis: Inferring evolutionary relationships by constructing trees from sketch-derived similarity measures.

Methodology:

Compute MinHash sketches of input DNA/RNA sequences and compare sketches using the Jaccard index.