scripts

• scripts/: This folder contains Python scripts dedicated to the workflow.
  • assign-clades-via-metadata.py: Uses provided metadata to assign clades to internal nodes and those with missing metadata.
  • assign-colors.py: Assigns colors to a variety of parameters if not already outlined in config files.
  • clades_renaming.py: Assigns clades and outbreak parameters to data notes.
  • combine_data_sources.py: Python script implemented before the release of 'augur merge'. This script is no longer used due to 'augur merge' being used in it's place.
  • construct-recency-from-submission-date.py: Script originally from https://github.com/nextstrain/ncov/blob/master/scripts/construct-recency-from-submission-date.py
  • fix_tree.py: Python script used for correcting and/or refining phylogenetic trees generated from genomic data.
  • mutation_context.py: Python script designed to analyze the genomic context of mutations within a set of sequences.
  • remove_timeinfo.py: Python script that returns the sample date in numeric form.
  • reverse_reversed_sequences.py: Python script designed to manipulate DNA or RNA sequences by reversing them and then reversing the order of the nucleotides within each sequence.
  • set_final_strain_name.py: Python scripts that swaps out the strain names in the Auspice JSON with the final strain name.