Shiny app for counting MinION reads (deployed at https://msierk.shinyapps.io/sequapath)
Sample input files are included in the input directory.
Requires an sqlite file nameNode.sqlite created by the taxonomizr R package (356 MB).
Uses rrnDB-5.6_pantaxa_stats_NCBI.tsv from https://rrndb.umms.med.umich.edu/static/download/
Uses PathogensDB.xlsx for labels of pathogenicity according to CDC, Robert Koch Institut, and Nephros: https://www.cdc.gov/hai/prevent/environment/water.html, https://www.bode-science-center.com/center/relevant-pathogens-from-a-z.html