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Simulation and validation

Teloscope includes a synthetic benchmark generator and evaluator in teloscope-simulate.

Build it with:

make simulate

The binary is written to build/bin/teloscope-simulate.

Generate synthetic assemblies

Example:

build/bin/teloscope-simulate -n 1000 -r 1e-4 -s 42 -o testFiles/simulate/rate_1e-4

This writes:

  • sequences.fa
  • ground_truth.tsv

Each synthetic sequence contains:

  1. left canonical telomere
  2. left TVR block
  3. random internal sequence
  4. right TVR block
  5. right canonical telomere

After the sequence is built, the requested mutation rate is applied across the whole sequence.

Evaluate Teloscope output

Run Teloscope on the synthetic FASTA, then compare the called terminal BED file to the ground truth:

build/bin/teloscope -f testFiles/simulate/rate_1e-4/sequences.fa -o testFiles/simulate/rate_1e-4/teloscope_out
build/bin/teloscope-simulate --evaluate \
  -g testFiles/simulate/rate_1e-4/ground_truth.tsv \
  -b testFiles/simulate/rate_1e-4/teloscope_out/sequences.fa_terminal_telomeres.bed

The evaluator prints:

  • total_tips
  • detected
  • sensitivity
  • mean_bias_bp
  • mean_abs_err_bp
  • tvr_rate
  • fp_blocks

Generator parameters

Flag Meaning Default
-n number of sequences 1000
-R canonical repeats per telomere end 2000
-T TVR repeats per telomere end 100
-L internal random segment length in bp 25000
-r per-base mutation rate 0.0
-s random seed 42
-o output directory testFiles/simulate

Sweep script

The repo includes a shell wrapper for mutation-rate sweeps:

bash .github/workflows/val-simulate.sh

Optional environment overrides:

SIM_N=1000000 SIM_SEED=42 bash .github/workflows/val-simulate.sh