R tools for Clostridioides difficile fluorescent PCR ribotyping. Matches query chromatograms (.fsa format) generated on capillary electrophoresis sequencers to a database of known C. difficile ribotypes.

Developed and maintained by the Walk Lab at Montana State University, Bozeman. Compatible with Mac OS X and Windows 10.

Download and install R (≥ 4.0): https://cran.r-project.org

Download Rtools (≥ 4.0): https://cran.r-project.org/bin/windows/Rtools/

Download RStudio Desktop (≥ 1.4): https://www.rstudio.com/products/rstudio/download/

Click the Code button on this page and select Download ZIP. Extract the contents to a directory on your computer.

1. Place .fsa files to analyze in the Files_to_analyze directory.
2. Open CdiffFragR.Rproj in RStudio.
3. Open Call_FSA.R via File > Open File…
4. Highlight all text and click Run.

After processing, each .fsa file is moved to Files_analyzed/. Results are written to a timestamped directory (Results_YYYY.MM.DD-Hour/) containing:

• chrom_*.jpeg — chromatogram summaries
• hits_*.jpeg — overlay plots comparing each query to its closest database match
• SUMMARY.csv — results table

Open SUMMARY.csv and review the Dist_1 column, which reports the Bray-Curtis dissimilarity between the query and the closest database match (0 = identical, 1 = completely dissimilar).

Good match — Solid match with a very low chance of a false positive.

Questionable match — May or may not be a match. Open the hit image and check whether peaks align (peaks within 1–2 bp should be considered the same).

Poor match — Not a match to the database. Check the chromatogram: either the ribotype is not yet in the database, or the sample should be re-analyzed.

If you believe you have identified a new ribotype, re-analyze to confirm, then contact the Walk Lab — we welcome additions to the database.

See cdifffragr_12.06.pdf for the full user manual.

GPL-3.0