Repositories list

• 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

  •2626 forks•6262 stars•4040 issues•1010 pull requests•Updated Apr 20, 2026Apr 20, 2026

• theiagen_docker_builds

  Public

  theiagen/theiagen_docker_builds’s past year of commit activity
  Python

  •

  GNU General Public License v3.0

  •00 forks•33 stars•11 issue•44 pull requests•Updated Apr 17, 2026Apr 17, 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

  •00 forks•66 stars•00 issues•00 pull requests•Updated Apr 16, 2026Apr 16, 2026

• theiavalidate

  Public
  A Python tool to compare the contents of two tab-delimited files.

  Python

  •

  GNU General Public License v3.0

  •11 fork•22 stars•11 issue•22 pull requests•Updated Apr 15, 2026Apr 15, 2026

• mycosnp-wdl

  Public
  A WDL wrapper of CDCGov/mycosnp-nf for Terra.bio

  WDL

  •

  Apache License 2.0

  •00 forks•33 stars•22 issues•11 pull request•Updated Apr 6, 2026Apr 6, 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

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• utilities

  Public
  A collection of general utility scripts

  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•11 star•00 issues•11 pull request•Updated Mar 15, 2026Mar 15, 2026

• test-datasets

  Public
  Test data to be used for automated testing with the nf-core pipelines

  MIT License

  •496496 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•11 star•22 issues•00 pull requests•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

  •137137 forks•00 stars•00 issues•00 pull requests•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

  •33 forks•00 stars•00 issues•00 pull requests•Updated Nov 5, 2025Nov 5, 2025

• TB-D

  Public
  Main repo linking all of Ash's tuberculosis projects

  WDL

  •22 forks•00 stars•00 issues•00 pull requests•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

  •66 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•44 stars•11 issue•00 pull requests•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

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 31, 2025Jul 31, 2025

• rabies

  Public
  Python

  •11 fork•11 star•00 issues•00 pull requests•Updated Jul 24, 2025Jul 24, 2025

• nf-theia

  Public
  Nextflow plugin for file tracking and reporting during workflow execution

  Groovy

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 22, 2025Jul 22, 2025

• setup-latch

  Public
  TypeScript

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jul 16, 2025Jul 16, 2025

• mbap-bacteria

  Public
  Nextflow

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 15, 2025Jul 15, 2025

• latch

  Public
  a python bioinformatics framework

  Python

  •

  MIT License

  •2222 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•11 star•00 issues•44 pull requests•Updated Apr 22, 2025Apr 22, 2025

• NE-PGCOE-Support

  Public
  Theiagen support for NorthEast Pathogen Genomic Center of Excellence efforts

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 16, 2025Apr 16, 2025

• RefNAAP-wdl

  Public
  WDL wrapper around https://github.com/jiangweiyao/RefNAAP

  HTML

  •

  Apache License 2.0

  •00 forks•00 stars•22 issues•00 pull requests•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

  •11 fork•11 star•00 issues•1111 pull requests•Updated Mar 31, 2025Mar 31, 2025

• theiaSoftClipPrimers

  Public
  Python

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 27, 2025Mar 27, 2025

• OHDL-AR-wdl

  Public
  OHDL_AR Workflow wrapped in WDL

  WDL

  •00 forks•11 star•00 issues•00 pull requests•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

  •381381 forks•00 stars•00 issues•00 pull requests•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

  •3232 forks•00 stars•00 issues•00 pull requests•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

  •11 fork•66 stars•00 issues•1010 pull requests•Updated Feb 27, 2025Feb 27, 2025

• AlleleCalling-wdl

  Public
  WDL

  •00 forks•00 stars•11 issue•00 pull requests•Updated Feb 14, 2025Feb 14, 2025