Bioinformatics workflows for characterization, epidemiology and sharing of pathogen genomes.
More information about the steps undertaken in these workflows is available via the Theiagen Public Resources Documentation.
Support for running these workflows can be sought by raising a GitHub issue or by contacting Theiagen at [email protected].
These workflows are written in WDL, a language for specifying data processing workflows with a human-readable and writeable syntax. They have been developed by Theiagen Genomics to primarily run on the Terra.bio platform but can be run locally or on an HPC system at the command-line with Cromwell or miniWDL.
- Based on collaborative work with Andrew Lang, PhD & his Genomic Analysis WDL workflows
- Workflows and task development influenced by The Broad's Viral Pipes
- TheiaCoV workflows for viral genomic characterization influenced by UPHL's Cecret & StaPH-B's Monroe
- TheiaProk workflows for bacterial genomic characterization influenced by Robert Petit's bactopia
- The PHB workflow user community. To provide feedback, please raise a GitHub issue.
Contributions to the workflows contained in this repository are warmly welcomed. Our style guide may be found here for convenience of formatting.
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.