Output Folder Structure

Some module implementations output extra files in the root of the output folder, but the following items can be found in most use-cases:

• CONFIG.json: A copy of the configuration file used in this execution of FAVITES (for reproducibility)
• contact_network.txt: The contact network that was simulated by FAVITES
• error_free_files: A directory containing all output of the error-free portion of the workflow
  • error_free_files/phylogenetic_trees: A directory containing all error-free phylogenetic trees (see File Formats for identifier information)
    • error_free_files/phylogenetic_trees/tree_#.time.tre: The error-free phylogenetic tree of the #-th transmission chain, in unit of time
    • error_free_files/phylogenetic_trees/tree_#.tre: The error-free phylogenetic tree of the #-th transmission chain, in unit of expected number of per-site mutations
    • error_free_files/phylogenetic_trees/merged_tree_#.time.tre: The #-th error-free merged phylogenetic tree, in unit of time
    • error_free_files/phylogenetic_trees/merged_tree_#.tre: The #-th error-free merged phylogenetic tree, in unit of expected number of per-site mutations
  • error_free_files/sequence_data.fasta: The complete set of all sampled viral sequences (see File Formats for identifier information)
  • error_free_files/transmission_network.gexf: The complete transmission network in the GEXF format
  • error_free_files/transmission_network.txt: The complete transmission network in the FAVITES edge list format
• error_prone_files: A directory containing all output of the error-prone portion of the workflow
  • error_prone_files/sequence_data_subsampled_errorfree.fasta: The sequencing dataset with subsampling errors imposed, but without sequencing errors in the FASTA format
  • error_prone_files/sequence_data_subsampled_errorprone*.fastq: The sequencing dataset with both subsampling and sequencing errors imposed in the FASTQ format
    • Some Sequencing module implementations will have multiple output FASTQ files, e.g. paired-end sequencing will have one FASTQ file for forward reads and another for reverse reads