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    35 repositories

    • utilities

      Public
      A collection of general utility scripts
      Shell
      •
      GNU Affero General Public License v3.0
      •0•1•0•1•Updated Feb 7, 2025Feb 7, 2025

    • 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
      •18•45•46•14•Updated Feb 7, 2025Feb 7, 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
      •0•2•0•1•Updated Feb 7, 2025Feb 7, 2025

    • mycosnp-wdl

      Public
      A WDL wrapper of CDCGov/mycosnp-nf for Terra.bio
      WDL
      •
      Apache License 2.0
      •0•2•3•2•Updated Feb 6, 2025Feb 6, 2025

    • OHDL-AR-wdl

      Public
      OHDL_AR Workflow wrapped in WDL
      WDL
      •0•0•0•0•Updated Feb 5, 2025Feb 5, 2025

    • theiagen_docker_builds

      Public
      Dockerfile
      •0•3•1•1•Updated Feb 3, 2025Feb 3, 2025

    • tbp-parser

      Public
      A TBProfiler output parser used to classify the severity of Mycobacterium tuberculosis mutations.
      tuberculosismycobacterium-tuberculosis-complexmycobacterium-tuberculosis
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Jan 31, 2025Jan 31, 2025

    • HMAS-wdl

      Public
      A WDL wrapper around HMAS-QC-Pipeline2 for Terra.bio
      WDL
      •0•1•1•1•Updated Dec 20, 2024Dec 20, 2024

    • RefNAAP-wdl

      Public
      WDL wrapper around https://github.com/jiangweiyao/RefNAAP
      HTML
      •0•0•0•0•Updated Dec 20, 2024Dec 20, 2024

    • docker-builds

      Public
      📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
      Dockerfile
      •
      GNU General Public License v3.0
      •128•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • mercury

      Public
      Mercury prepares and formats metadata for submission to national & international genomic databases.
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Oct 25, 2024Oct 25, 2024

    • AlleleCalling-wdl

      Public
      WDL
      •0•0•1•0•Updated Sep 27, 2024Sep 27, 2024

    • stylo-wdl

      Public
      WDL
      •0•1•0•0•Updated Sep 17, 2024Sep 17, 2024

    • NE-PGCOE-Support

      Public
      Theiagen support for NorthEast Pathogen Genomic Center of Excellence efforts
      0•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • public_health_viral_genomics

      Public
      Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
      WDL
      •
      GNU Affero General Public License v3.0
      •17•42•15•1•Updated Aug 5, 2024Aug 5, 2024

    • Western-WFD-2024

      Public
      Resource for the Western Region WFD 2024 Training Event
      Shell
      •
      GNU General Public License v3.0
      •3•0•0•12•Updated Jul 31, 2024Jul 31, 2024

    • dev-assessment

      Public
      WDL
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • terra_utilities

      Public
      WDL
      •
      GNU Affero General Public License v3.0
      •1•4•2•2•Updated May 17, 2024May 17, 2024

    • VADR_models

      Public
      Batchfile
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Mar 21, 2024Mar 21, 2024

    • theiavalidate

      Public
      A Python tool to compare the contents of two tab-delimited files.
      Python
      •
      GNU General Public License v3.0
      •1•2•3•0•Updated Jan 29, 2024Jan 29, 2024

    • read_scrub_benchmark

      Public
      WDL workflow to compare host removal tools
      WDL
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 22, 2023Sep 22, 2023

    • public_health_bacterial_genomics

      Public
      WDL
      •
      GNU Affero General Public License v3.0
      •14•27•32•0•Updated Aug 2, 2023Aug 2, 2023

    • centroid

      Public
      tool to determine optimal refrerence genome given a set of fasta files
      Python
      •3•0•0•0•Updated May 18, 2023May 18, 2023

    • MGen-Theiagen-2023

      Public
      R
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Feb 8, 2023Feb 8, 2023

    • pb-hifi-viral

      Public
      WDL and dockerfiles for tools related to PacBio's HiFi Viral SARS-CoV-2 sequence analysis
      WDL
      •0•0•0•0•Updated Dec 22, 2022Dec 22, 2022

    • staphb.org

      Public
      HTML
      •0•0•0•11•Updated Dec 7, 2022Dec 7, 2022

    • wm_training_202205

      Public template
      Theiagen Genomics repository for workflow management training
      Nextflow
      •
      GNU General Public License v3.0
      •3•5•0•1•Updated Oct 6, 2022Oct 6, 2022

    • wm_training_202207

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 10, 2022Jun 10, 2022

    • rhea

      Public
      SARS-CoV-2 consensus assembly quality check and corrections.
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•1•0•Updated Jan 7, 2022Jan 7, 2022

    • bacterial-characterization

      Public
      WDL
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2021Apr 30, 2021