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    • Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
      WDL
      25613611Updated Feb 24, 2026Feb 24, 2026
    • Dockerfile
      0314Updated Feb 24, 2026Feb 24, 2026
    • utilities

      Public
      A collection of general utility scripts
      Python
      0102Updated Feb 20, 2026Feb 20, 2026
    • A TBProfiler output parser used to classify the severity of Mycobacterium tuberculosis mutations.
      Python
      0611Updated Feb 19, 2026Feb 19, 2026
    • A Python tool to compare the contents of two tab-delimited files.
      Python
      1211Updated Dec 3, 2025Dec 3, 2025
    • Test data to be used for automated testing with the nf-core pipelines
      461000Updated Dec 2, 2025Dec 2, 2025
    • A collection of python-based phylogenetic analysis and comparison tools
      Python
      0120Updated Nov 13, 2025Nov 13, 2025
    • :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
      Dockerfile
      137000Updated Nov 5, 2025Nov 5, 2025
    • tree_nine

      Public
      Put diff files on an existing phylo tree using UShER and taxonium tools.
      Python
      3000Updated Nov 5, 2025Nov 5, 2025
    • TB-D

      Public
      Main repo linking all of Ash's tuberculosis projects
      WDL
      2000Updated Nov 5, 2025Nov 5, 2025
    • myco

      Public
      WIP pipeline built for phylogenic analysis of the Mycobacterium tuberculosis complex (MBTC)
      PureBasic
      6000Updated Nov 5, 2025Nov 5, 2025
    • mercury

      Public
      Mercury prepares and formats metadata for submission to national & international genomic databases.
      Python
      0410Updated Aug 20, 2025Aug 20, 2025
    • A WDL wrapper of CDCGov/mycosnp-nf for Terra.bio
      WDL
      0320Updated Aug 11, 2025Aug 11, 2025
    • Theiaprok illumina pe build out for nextflow
      Nextflow
      0200Updated Jul 31, 2025Jul 31, 2025
    • rabies

      Public
      Python
      1100Updated Jul 24, 2025Jul 24, 2025
    • nf-theia

      Public
      Nextflow plugin for file tracking and reporting during workflow execution
      Groovy
      0000Updated Jul 22, 2025Jul 22, 2025
    • TypeScript
      3000Updated Jul 16, 2025Jul 16, 2025
    • Nextflow
      0000Updated Jul 15, 2025Jul 15, 2025
    • latch

      Public
      a python bioinformatics framework
      Python
      22000Updated Jul 15, 2025Jul 15, 2025
    • Resource for Mid-Atlantic's Docker for Public Health Bioinformatics 2025 Training Event
      Dockerfile
      1104Updated Apr 22, 2025Apr 22, 2025
    • Theiagen support for NorthEast Pathogen Genomic Center of Excellence efforts
      0000Updated Apr 16, 2025Apr 16, 2025
    • WDL wrapper around https://github.com/jiangweiyao/RefNAAP
      HTML
      0020Updated Apr 3, 2025Apr 3, 2025
    • About Resource for Northeast's Software Development Practices for Public Health Bioinformatics 2025 Training Event
      Nextflow
      11011Updated Mar 31, 2025Mar 31, 2025
    • Python
      0000Updated Mar 27, 2025Mar 27, 2025
    • OHDL_AR Workflow wrapped in WDL
      WDL
      0100Updated Mar 17, 2025Mar 17, 2025
    • Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      Scala
      378000Updated Mar 13, 2025Mar 13, 2025
    • fiss

      Public
      FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine
      Python
      32000Updated Mar 1, 2025Mar 1, 2025
    • Resource for Mid-Atlantic's Software Development Practices for Public Health Bioinformatics 2025 Training Event
      Nextflow
      16010Updated Feb 27, 2025Feb 27, 2025
    • WDL
      0010Updated Feb 14, 2025Feb 14, 2025
    • HMAS-wdl

      Public
      A WDL wrapper around HMAS-QC-Pipeline2 for Terra.bio
      WDL
      0111Updated Dec 20, 2024Dec 20, 2024