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Purpose & Workflows¶
The PHB repository contains workflows for the characterization, genomic epidemiology, and sharing of pathogen genomes of public health concern. Workflows are available for viruses, bacteria, and fungi.
All workflows in the PHB repository end with _PHB
in order to differentiate them from earlier versions and from the original tools they incorporate.
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Command-line Users
Learn how to use our workflows on the command-line!
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Terra Users
Learn how to use our workflows on Terra!
Our Open Source Philosophy
PHB source code is publicly available on GitHub and available under GNU Affero General Public License v3.0!
All workflows can be imported directly to Terra via the Dockstore PHB collection!
You can also use our workflows on the command-line. Please see our guide on how to get started here!
When undertaking genomic analysis using the command-line, via Terra, or other data visualization platforms, it is essential to consider the necessary and appropriate workflows and resources for your analysis. To help you make these choices, take a look at the relationship between the most commonly used Theiagen workflows.
PHB development is a cycle¶
We continuously work to improve our codebase and usability of our workflows by the public health community, so changes from version to version are expected. This documentation page reflects the state of the workflow at the version stated in the title.
What's new?
You can see the changes since PHB v2.2.1 here!
Contributing to the PHB Repository¶
We warmly welcome contributions to this repository! Our style guide may be found here for convenience of formatting.
If you would like to submit suggested code changes to our workflows, you may add or modify the WDL files and submit pull requests to the PHB GitHub repository.
You can expect a careful review of every PR and feedback as needed before merging, just like we do for PRs submitted by the Theiagen team. Our PR template can help prepare you for the review process. As always, reach out with any questions! We love recieving feedback and contributions from the community. When your PR is merged, we'll add your name to the contributors list below!
Authorship & Responsibility¶
Authorship¶
(Ordered by contribution [# of lines changed] as of 2024-12-04)
- Sage Wright (@sage-wright) - Conceptualization, Software, Validation, Supervision
- Inês Mendes (@cimendes) - Software, Validation
- Curtis Kapsak (@kapsakcj) - Conceptualization, Software, Validation
- Frank Ambrosio (@frankambrosio3) - Conceptualization, Software, Validation
- Michelle Scribner (@michellescribner) - Software, Validation
- Kevin Libuit (@kevinlibuit) - Conceptualization, Project Administration, Software, Validation, Supervision
- Fraser Combe (@fraser-combe) - Software, Validation
- Andrew Page (@andrewjpage) - Project Administration, Software, Supervision
- Michal Babinski (@Michal-Babins) - Software, Validation
- Andrew Lang (@AndrewLangVt) - Software, Supervision
- Kelsey Kropp (@kelseykropp) - Validation
- Joel Sevinsky (@sevinsky) - Conceptualization, Project Administration, Supervision
External Contributors¶
We would like to gratefully acknowledge the following individuals from the public health community for their contributions to the PHB repository:
- James Otieno (@jrotieno)
- Robert Petit (@rpetit3)
- Emma Doughty (@emmadoughty)
- Ash O'Farrel (@aofarrel)
- Sam Baird (@sam-baird)
- Holly Halstead (@HNHalstead)
- Emily Smith (@emily-smith1)
On the Shoulder of Giants¶
The PHB repository would not be possible without its predecessors. We would like to acknowledge the following repositories, individuals, and contributors for their influence on the development of these workflows:
The PHB repository originated from collaborative work with Andrew Lang, PhD & his Genomic Analysis WDL workflows. The workflows and task development were influenced by The Broad's Viral Pipes repository. The TheiaCoV workflows for viral genomic characterization were influenced by UPHL's Cecret & StaPH-B's Monroe (now deprecated) workflows. The TheiaProk workflows for bacterial genomic characterization were influenced by Robert Petit's bactopia. Most importantly, the PHB user community drove the development of these workflows and we are grateful for their feedback and contributions.
If you would like to provide feedback, please raise a GitHub issue or contact us at support@theiagen.com.
Maintaining PHB Pipelines¶
Theiagen Genomics has committed to maintaining these workflows for the forseeable future. These workflows are written using a standard workflow language (WDL) and uses Docker images based on the StaPHB-B Docker Builds. New versions that include bug fixes and additional features are released on a quarterly bases, with urgent bug fixes released as needed. Each version is accompanied by detailed release notes to lower the barrier of pipeline upkeep from the public health community at large.
Point of Contact¶
If you have any questions or concerns, please raise a GitHub issue or email Theiagen's general support at support@theiagen.com.
Conflict of Interest¶
The authors declare no conflict of interest.
Citation¶
Please cite this paper if publishing work using any workflows:
Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. "Accelerating Bioinformatics Implementation in Public Health." Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051.
Alternatively, please cite this paper if using the TheiaEuk workflow:
Ambrosio, Frank, Michelle Scribner, Sage Wright, James Otieno, Emma Doughty, Andrew Gorzalski, Danielle Siao, et al. 2023. "TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization." Frontiers in Public Health 11. https://doi.org/10.3389/fpubh.2023.1198213.
About Theiagen¶
Theiagen develops bioinformatics solutions for public health labs, and then trains and supports scientists to use these. If you would like to work with Theiagen, please get in contact.