This Github repository contains the reproducible analyses and data for the manuscript titled "Serovar-level Detection of Bacterial Foodborne Pathogens Using Long-read Amplicon Sequencing".

Required files for analysis and pre-built analysis files can be found in the /Files directory on this main page. The Seroplacer Core Files are required for replicating the analysis found in this work, and the Figure 1 and Figure 4 files contain pre-built data which is computationally time consuming to run, in order to save time for replicating results.

The full reproducible analysis can be found in a pre-rendered HTML file available for each section of the analysis, described below, along with supporting information:

Directory of Relevant Manuscript Files

• Seroplacer Analysis of Salmonella Test Data.
• Seroplacer Analysis of E. coli Test Data.
• Analysis of Isolate and Environmental Sample Data.
• Salmonella Database Construction (R Scripts)
• E. coli Database Construction (R Scripts)
• Full Salmonella and E. coli Aligned FASTA Files

Dmitry Grinevich ([email protected])