The Walk lab offers online data analysis tools for capillary electrophoresis (Sanger-style sequencer)based fragment analysis. These products were developed with funding support from the US National Institutes of Health and the National Institute of Allergy and Infectious Diseases (1K01AI097281). Use the links below to get started and feel free to contact us if you have any questions!
1. Fluorescent PCR ribotyping analysis pipeline
Clostridioides difficile is a Gram-positive bacterium species that can colonize and sometimes cause infections in the human gut. C. difficile infection is now the leading healthcare-associated infections among US hospitals and a worldwide cause of morbidity and mortality. Fluorescent PCR ribotyping is a low cost, genotyping assay for the identification of specific C. difficile lineages. We originally described our protocol here and validated data portabilty across laboratories and sequencing centers here.
We generated an analysis pipeline that requires no proprietary software to view chromatogram files and search for matches against our database of 123 different ribotypes.
Download our BRIEF MANUAL to see how it works and download the CdiffFragR program here.
***Naming conventions have been generally consistent but if you need to compare results obtained prior to 8/2016, check out the LegacyMap.
When using this pipeline, it is important that you download the latest version of the C. difficile ribotype database. We will keep track of versions here:
|Current Version:||Release Date:|
2. Fluorescent PCR ribotyping chromatograms
The analysis tool above compares data in chromatograms from a capillary sequencer to data in an online database. It is meant to streamline analysis of large sets of data. That said, visual comparison between chromatograms remains the best way to identify existing and novel C. difficile ribotypes (i.e. Gold standard). To facilitate visual comparisons, we provided a subset of chromatograms for download.