The URDO project has he goal of improving detection and diagnosis of respiratory pathogens,
including bacteria like Bordetella pertussis and Legionella pneumophila, as well as viruses such as influenza
and Middle East respiratory syndrome (MERS). To do this, the CDC has been collaborating with other state public health
laboratories to develop a chip-based multiplexed PCR assay, which will be followed by next-generation sequencing
and bioinformatics analysis for pathogen detection (which microbe is this?) and characterization (for e.g., typing,
searching for resistance genes, etc).
The CDC team is led by Jonas Winchell at the CDC National Center for Immunization and Respiratory Diseases (NCIRD), and
the two state laboratories involved include the Massachusetts State Laboratory and Minnesota Department of Public Health.
The URDO project utilized k-mer-based methods for pathogen detection and characterization. Since the project
remains unpublished, these bioinformatic pipelines have been removed from the repository and its history
via BFG before migration (from the CDC internal gitlab to github).
Tiffany specifically worked on two parts of the project:
- PCR primer generation for human rhinovirus for the chip-based multiplexed PCR
- Visualization of the bioinformatics results
Instructions for primer generation are located within the primers folder, while the script for visualization is located
in kmer/visualization.