Supplementary data for CRISPR spacer-protospacer matching benchmarks

Dataset Overview Benchmark inputs, raw tool outputs, and logs for CRISPR spacer–protospacer matching benchmarks (real and simulated sets). Raw outputs and subsampled/simulated inputs are included; large intermediate tools_results.tsv tables are omitted to keep size manageable. Logs, SLURM logs, and job/bash scripts are preserved for reproducibility. For more information, see the github repository:https://github.com/UriNeri/spacer_matching_bench Note - the files below serve as the input for the actual per-tool comparison. The:multi_metric_distances.parquet and performance_results_hamming_mm5.tsv are only some of the files generated using the raw tool outputs. TO recreate the per-metric, up to n distance, per alignment / region, results, you can see the notebooks in the github repository (for example in the 3rd code cell in Performance_simulated_v2.ipynb , or via the Regenerate_multimetric_files.ipynb notebook). Note that the code version producing these should be consistent up to commit bdf114c. Archive Files real_data_v2.tar.zst simulated_data_v2.tar.zst Contents and Structure real_data_v2.tar.zst └── results/real_data/subsamples/ ├── fraction_0.0005/ │ ├── raw_outputs/ # per-tool SAM/TSV raw results │ ├── subsampled_data/ # inputs: contigs for this fraction (fasta) and their metadta (tsv, from img/vr) │ ├── logs/ # the benchmark CLI run logs (includes spot checked alignment tracebacks) │ ├── slurm_logs/ # SLURM outputs (stdout/stderr) │ ├── bash_scripts/ # bash launchers (one per tool) │ ├── job_scripts/ # per-tool job submission ("sbatch") scripts │ ├── multi_metric_distances.parquet # │ └── performance_results_hamming_mm5.tsv ├── fraction_0.001/ ├── fraction_0.005/ ├── fraction_0.01/ ├── fraction_0.05/ ├── fraction_0.1/ └── fraction_1/ simulated_data_v2.tar.zst └── results/simulated/ ├── ns_100_nc_5000/ ├── ns_500_nc_5000_HIGH_INSERTION_RATE/ ├── ns_50000_nc_5000/ ├── ns_75000_nc_5000/ ├── ns_100000_nc_10000/ ├── ns_100000_nc_20000/ ├── ns_3826979_nc_421431_real_baseline/ └── ns_500000_nc_100000/ ├── raw_outputs/ # per-tool SAM/TSV raw results ├── simulated_data/ | ├── planned_ground_truth.tsv # locations and number of substitions for each location a spacer was inserted into a contig | ├── simulated_contigs.fa | └── simulated_spacers.fa ├── slurm_logs/ ├── logs/ ├── bash_scripts/ ├── job_scripts/ ├── multi_metric_distances.parquet └── performance_results_hamming_mm5.tsv