Tools

The Walk lab offers online tools for colleagues seeking the following analyses and data. 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 analyze your data using our server. Feel free to contact us if you have any questions!

1. Fluorescent PCR ribotyping analysis pipeline

Clostridium difficile is a bacterial species that can infect the human gut. C. difficile infection is now the leading healthcare-acquired infectious disease among US hospitals and it is a worldwide cause of morbidity and mortality. Fluorescent PCR ribotyping is a low cost, genotyping assay for the identification of pathogenic C. difficile strains. We originally described our protocol here and validated data portabilty across laboratories and sequencing centers here.

In general, two types of users will be served by this database:
– users that request comparison to the database only (no participation in curation); and,
– users that request participation in curation of the database by submitting C. difficile isolates that represent new fluorescent PCR ribotypes.

Please contact us if you would like to submit your data or isolates to the database. Your help will ensure that this resource is representative of all C. difficile pathogens.

Download the protocol to see how it works. Check out the FAQ.

***PREVIOUS USERS (prior to 8/8/2016): We recently updated our ribotyping nomenclature to be consistent with the C. difficile ribotyping network in the UK. Here is a LegacyMap, so that you can keep track of all the changes.

Access the server and submit data for analysis.

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 C. difficile ribotypes (i.e. Gold standard) and to make calls between similar looking chromatograms. To facilitate visual comparisons, we provided a subset of chromatograms for download.

Access the server and request chromatograms.