3. Tutorial (Advanced Settings)

SIRIUS flags continued.

1. --soft_rscu= boolean value (true/false) [Default: false]

   • Specify if you would like to provide a soft cut-off for codons with an RSCU value under this threshold. Switching this flag to true requires you to also specify the following:
     • --codon_usage_fpath= string value [No default – This is required]
       • Path to the .csv file containing amino acid codes, their codons, and the respective RSCU values. See TODO for an example file.
     • --rscu_threshold= positive floating point value between 0-1 [Default = 0.5]
       • Codons with an RSCU below this value might be excluded from the output genes. If not provided by you, a default value is used. See the mathematical explanation below on how this flag behaves.
     • --max_low_rscu_ratio= floating point value between 0-1 [Default = 0.3]
       • TODO
     • --rscu_alpha= floating point value > 0 [Default = 10.0]
       • TODO

2. --num_workers= integer value > 0 [Default = 16]

   • Specify the number of threads available to the Google OR-Tools solver. A value between 16-32 is ideal. Higher values may actually slow the solve.

3. --show_ortools_log= boolean value (true/false) [Default: false]

   • When true, outputs the Google OR-Tools logs.

4. --relative_gap_limit= floating point value between 0-1 [Default = 0.0]

   • A larger value tells the solver to accept a sub-optimal solution. Only increase this (and slightly, perhaps starting with 0.1, which is 10%) if you are experiencing high solve times.

5. --cai

   • TODO

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The third way to run SIRIUS is via the config.yaml file. Note that any flags passed to SIRIUS will cause the program to ignore all settings in the config.yaml, and instead only use those flags.

TODO

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Mathematics for Soft RSCU

TODO