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  1. THRESHER THRESHER Public

    THRESHER is a framework that replaces fixed cutoffs with data-driven phylothresholds - the SNP thresholds corrected for phylogenetic topology and inferred directly from each dataset's genomic struc…

    R 14

  2. CURED CURED Public

    Python 1 1

  3. DAMAGE DAMAGE Public

    Diagnostic Allele Method for Actionable Genomic Epidemiology

    R 1

  4. Redcarpet Redcarpet Public

    Python 1

  5. WhatsGNU-ATB WhatsGNU-ATB Public

    A custom reimplementation of WhatsGNU optimised for the scale of AllTheBacteria. It uses LMDB-backed sharded storage (8 shards) with numpy for hashing. The query tool is also custom-built for this …

    Python

  6. SILOSim SILOSim Public

    A data-driven framework that profiles per-site bacterial genome variability and simulates evolution from it. From a single genome assembly, SILOSim builds a map of per-site entropy and mobile genet…

    Python

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