benchmarking.md

This part of the paper describes the benchmarking over the simulations using Decoil, Shasta and CReSIL.

2.3 Alignment-free ecDNA reconstruction using Shasta from simulated data

cd simulation_benchmarking/benchmarking/shasta
bash install.sh

# run Shasta for the simulations
sbatch run_shasta.sh

2.4 Alignment-based ecDNA reconstruction using Decoil from simulated data

cd simulation_benchmarking/benchmarking/decoil
bash install.sh

# run Shasta for the simulations
sbatch run_decoil.sh <root> <ref> <anno>

2.5 Alignment-based ecDNA reconstruction using CReSIL from simulated data

cd simulation_benchmarking/benchmarking/cresil
bash install.sh

# run CReSIL for the simulations
sbatch run_cresil.sh

2.6 Performance evaluation on simulated data for Decoil, Shasta and CReSIL

cd simulation_benchmarking/benchmarking/quast

# install Quast
bash install.sh

# run Quast for Decoil, Shasta and CReSIL for the simulations
sbatch run_quast_decoil.sh <rootdir>
sbatch run_quast_shasta.sh <rootdir>
sbatch run_quast_cresil.sh <rootdir>

# collect all results
# output: collect_metrics.txt
bash run_collect_metrics.sh

The output is collect_metrics.txt (https://doi.org/10.5281/zenodo.10785693).