Configuration manual

simAIRR arguments

Argument	Description	Type	Required	Default
mode	One of the four possible modes to use simAIRR	str	True	None; Legal options: ‘baseline_repertoire_generation’ ‘public_component_correction’ ‘signal_implantation’ ‘signal_feasibility_assessment’
olga_model	One of the four possible V(D)J recombination models supplied with Olga tool	str	True	None; Legal options: ‘humanTRA’ ‘humanTRB’ ‘humanIGH’ ‘mouseTRB’
output_path	Path to the output directory	str	False	./simairr_output
n_repertoires	Number of desired repertoires	int	True	None
seed	A seed to be set if simulations need to be reproducible	int	False	No reproducible seed
n_sequences	Approximate and minimum number of sequences desired in each repertoire	int	True	None
depth_variation	whether to have poisson variation around desired number of sequences (applicable only in baseline repertoire generation mode)	bool	False	False
background_sequences_path	path to a file containing background sequences that will be used for the construction of baseline repertoires instead of a OLGA V(D)J model	str	False	None
n_threads	Number of processes (reduces execution time at the expense of using more of the available CPUs	int	True	None
public_seq_proportion	The proportion of the total unique sequences in repertoire dataset to be shared across repertoires (a value between 0 and 1)	float	False	0.1
public_seq_pgen_count_mapping_file	Path to the file in the suggested format with empirical relation between generation probability and population incidence of public sequences	str	False	Empirical relation derived based on public sequence data from Emerson et al., 2017
signal_pgen_count_mapping_file	Path to the file in the suggested format with empirical relation between generation probability and population incidence of signal sequences	str	False	Empirical relation derived based on reported signal data from Emerson et al., 2017
signal_sequences_file	Path to the file with signal sequences (in OLGA format)	str	True	None
positive_label_rate	Proportion of desired repertoires to receive signal implantation	float	False	0.5
phenotype_burden	Average number of signal sequences each positive class labeled repertoire should carry	int	True	None
phenotype_pool_size	Desired number of sequences to be used for signal implantation (if a large pool of sequences are supplied initially)	int	False	Minimum number of sequences sufficient to meet desired phenotype burden will be chosen
allow_closer_phenotype_burden	If signal implantation was found infeasible precisely at the desired phenotype burden, whether to allow signal implantation at a closer phenotype burden	bool	False	True
store_intermediate_files	whether to store all the intermediate files that were generated and used as the basis for simulated repertoires	bool	False	False
negative_control	whether baseline repertoires are intended as negative control	bool	False	False
export_nt	whether to export nucleotide sequences in simulated repertoires	bool	False	True; Exception: False when no nucleotide sequences supplied in user-supplied signal sequences