Code for identifying resistance mutations in Sars-Cov-2 against 3CLpro and RdRp based on the Stanford Sars-Cov-2 database

Currently only the create_BN_import_nanopore.R script is relevant (for Illumina, MIK or other external HF see create_BN_import.R or create_BN_import_sihf.R). Also, we only create a BN import file for 3Clpro mutations. Although the code can be used to identify any RdRP resistance mutations as well.

Possible future developments:

• Use the Stanford SQL database and extract relevant information. See for example here, here and here.
• Integrate code with other routine analysis.
• Run the code "oppsett" by "oppsett" whenever we get new results.