simulate-data CLI

Input Parameters to simulate-data

Careful tuning of the following parameters allows the simulation to match the empirical error profile of specific sequencing platforms or chemistries.

CLI Option	Type	What It Controls	Default
model_name	TEXT	Library model key defining segment order and motifs	required
output_dir	TEXT	Output directory for simulated data (simulated_data/)	required
--training-seq-orders-file	TEXT	Path to training_seq_orders.tsv defining segment order and sequences	utils/training_seq_orders.tsv
--num-reads	INT	Number of primary reads to simulate (before reverse-complement doubling)	50000
--mismatch-rate	FLOAT	Base substitution probability during training read simulation	0.05
--insertion-rate	FLOAT	Base insertion probability during training read simulation	0.05
--deletion-rate	FLOAT	Base deletion probability during training read simulation	0.06
--min-cdna	INT	Minimum cDNA length used in training read simulation	100
--max-cdna	INT	Maximum cDNA length used in training read simulation	500
--polyt-error-rate	FLOAT	Error rate within polyA/polyT segments during training simulation	0.02
--max-insertions	INT	Maximum number of insertions allowed after a single base	1
--threads	INT	CPU threads used for training read simulation	2
--rc / --no-rc	FLAG	Include reverse-complemented reads (doubles training set size)	--rc
--transcriptome	TEXT	Transcriptome FASTA used for cDNA generation (else random transcripts)	None
--invalid-fraction	FLOAT	Fraction of training reads generated as invalid/artifactual	0.3
--help	FLAG	Show help message	—

Example Use Case

tranquillyzer simulate-data \
    10x3p_sc_ont \
    training_out \
    --num-reads 50000 \
    --mismatch-rate 0.05 \
    --insertion-rate 0.05 \
    --deletion-rate 0.06 \
    --min-cdna 100 \
    --max-cdna 500 \
    --polyt-error-rate 0.02 \
    --max-insertions 1 \
    --invalid-fraction 0.3 \
    --rc \
    --threads 2 \
    --transcriptome gencode.v44.transcripts.fa