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@theiagen Theiagen Genomics

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    53 repositories

    • public_health_bioinformatics

      Public
      Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
      WDL
      •
      GNU General Public License v3.0
      •26•63•18•8•Updated Jul 3, 2026Jul 3, 2026

    • magenelearn-wdl

      Public
      WDL wrapper for MaGeneLearn tool
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 2, 2026Jul 2, 2026

    • theiavalidate

      Public
      A Python tool to compare the contents of two tab-delimited files.
      Python
      •
      GNU General Public License v3.0
      •1•2•1•1•Updated Jul 2, 2026Jul 2, 2026

    • theiagen_docker_builds

      Public
      Python
      •
      GNU General Public License v3.0
      •0•3•0•4•Updated Jul 2, 2026Jul 2, 2026

    • utilities

      Public
      A collection of general utility scripts
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•1•Updated Jun 12, 2026Jun 12, 2026

    • tbp-parser

      Public
      A TBProfiler output parser used to classify the severity of Mycobacterium tuberculosis mutations.
      tuberculosismycobacterium-tuberculosis-complexmycobacterium-tuberculosis
      tuberculosismycobacterium-tuberculosis-complexmycobacterium-tuberculosis
      Python
      •
      GNU General Public License v3.0
      •0•6•0•0•Updated May 21, 2026May 21, 2026

    • mycosnp-wdl

      Public
      A WDL wrapper of CDCGov/mycosnp-nf for Terra.bio
      WDL
      •
      Apache License 2.0
      •0•3•0•0•Updated Apr 30, 2026Apr 30, 2026

    • nocasim

      Public
      Generates realistic paired-end FASTQ from simulated hybrid capture enrichment of Norovirus VP1.
      enrichmenthybrid-capturenorovirus
      enrichmenthybrid-capturenorovirus
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 18, 2026Mar 18, 2026

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •518•0•0•0•Updated Dec 2, 2025Dec 2, 2025

    • theiaphylo

      Public
      A collection of python-based phylogenetic analysis and comparison tools
      Python
      •
      GNU General Public License v3.0
      •0•1•2•0•Updated Nov 13, 2025Nov 13, 2025

    • docker-builds

      Public
      :package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
      Dockerfile
      •
      GNU General Public License v3.0
      •138•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • tree_nine

      Public
      Put diff files on an existing phylo tree using UShER and taxonium tools.
      Python
      •
      MIT License
      •3•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • TB-D

      Public
      Main repo linking all of Ash's tuberculosis projects
      WDL
      •2•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • myco

      Public
      WIP pipeline built for phylogenic analysis of the Mycobacterium tuberculosis complex (MBTC)
      PureBasic
      •
      GNU General Public License v3.0
      •6•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • mercury

      Public
      Mercury prepares and formats metadata for submission to national & international genomic databases.
      Python
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Aug 20, 2025Aug 20, 2025

    • theiaprok_illumina_pe-nf

      Public
      Theiaprok illumina pe build out for nextflow
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jul 31, 2025Jul 31, 2025

    • rabies

      Public
      Python
      •2•1•0•0•Updated Jul 24, 2025Jul 24, 2025

    • nf-theia

      Public
      Nextflow plugin for file tracking and reporting during workflow execution
      Groovy
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • setup-latch

      Public
      TypeScript
      •
      MIT License
      •3•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • mbap-bacteria

      Public
      Nextflow
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • latch

      Public
      a python bioinformatics framework
      Python
      •
      MIT License
      •23•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • Mid-Atlantic-Docker4PH-2025

      Public
      Resource for Mid-Atlantic's Docker for Public Health Bioinformatics 2025 Training Event
      Dockerfile
      •1•1•0•4•Updated Apr 22, 2025Apr 22, 2025

    • NE-PGCOE-Support

      Public
      Theiagen support for NorthEast Pathogen Genomic Center of Excellence efforts
      0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • RefNAAP-wdl

      Public
      WDL wrapper around https://github.com/jiangweiyao/RefNAAP
      HTML
      •
      Apache License 2.0
      •0•0•2•0•Updated Apr 3, 2025Apr 3, 2025

    • Northeast-SDP4PHB-2025

      Public
      About Resource for Northeast's Software Development Practices for Public Health Bioinformatics 2025 Training Event
      Nextflow
      •
      GNU General Public License v3.0
      •1•1•0•11•Updated Mar 31, 2025Mar 31, 2025

    • theiaSoftClipPrimers

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • OHDL-AR-wdl

      Public
      OHDL_AR Workflow wrapped in WDL
      WDL
      •0•1•0•0•Updated Mar 17, 2025Mar 17, 2025

    • cromwell_aws

      Public
      Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
      Scala
      •
      BSD 3-Clause "New" or "Revised" License
      •382•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • fiss

      Public
      FireCloud Service Selector (FISS) -- Python bindings and CLI for FireCloud execution engine
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •32•0•0•0•Updated Mar 1, 2025Mar 1, 2025

    • Mid-Atlantic-SDP4PHB-2025

      Public
      Resource for Mid-Atlantic's Software Development Practices for Public Health Bioinformatics 2025 Training Event
      Nextflow
      •
      GNU General Public License v3.0
      •1•6•0•10•Updated Feb 27, 2025Feb 27, 2025
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