TopoEdit-Off is a source-aware benchmark resource for high-mismatch genome-editing off-target prioritization.
This repository contains the public software/resource release accompanying the manuscript:
TopoEdit-Off: a source-aware benchmark for high-mismatch genome-editing off-target prioritization
TopoEdit-Off organizes public genome-editing off-target evidence into a compact, source-aware benchmark. The resource is designed to support:
- comparison of conventional nuclease, TOPO-seq, and base-editor observed-positive spaces;
- mismatch-regime analysis across evidence sources;
- size-matched top-K ranking evaluation;
- validation-priority panel design;
- reproducible access to compact benchmark summaries and release metadata.
This repository is intentionally minimal. It contains public-facing summary tables, ranking summaries, validation-priority panels, manifests, checksums, and a minimal smoke test. Large candidate-level derived tables are not stored in this GitHub repository.
| Item | Value |
|---|---|
| Guide panel | 100 guides |
| Generated candidate universe | 1,961,227 rows |
| Source-aware known-positive rows | 25,457 rows |
| Mismatch-6 candidate rows | 1,637,800 rows |
| TOPO source-positive guide support | 6 guides |
| Source-aware base-editor-positive guide support | 11 guides |
| Core validation-priority panel | 96 candidates |
data/benchmark/ Core source-aware benchmark summaries
data/ranking/ Size-matched top-K ranking evaluation
data/validation_panels/ Validation-priority candidate panels
demo/ Minimal smoke test
metadata/ File manifest, checksums, and data dictionary
tools/ Lightweight release validator
| Path | Purpose |
|---|---|
data/benchmark/source_aware_label_inventory.tsv |
Summary of source-aware label counts |
data/benchmark/mismatch_bucket_coverage.tsv |
Mismatch-regime coverage by label subset |
data/benchmark/candidate_burden_by_family.tsv |
Candidate burden by evidence family |
data/ranking/size_matched_topk_recovery_summary.tsv |
Size-matched observed-positive recovery at top K |
data/ranking/delta_vs_sequence_baseline_summary.tsv |
Change in recovery relative to the sequence baseline |
data/ranking/rank_methods.tsv |
Ranking methods used in the public summary |
data/ranking/metric_definitions.tsv |
Metric definitions and interpretation notes |
data/validation_panels/validation_panel_core96.tsv |
Core validation-priority panel |
data/validation_panels/panel_tier_summary.tsv |
Core, expanded, and backup panel sizes |
The demo checks that the public release is readable and internally consistent. It does not rerun the full candidate-generation or model-training pipeline.
python -m pip install pandas
python demo/run_minimal_demo.py
cat demo/output/minimal_demo_summary.mdExpected generated files:
demo/output/minimal_demo_summary.md
demo/output/top1000_recovery_summary.tsv
Run the repository validator:
python tools/validate_release.py --root .Expected result:
[PASS] minimal TopoEdit-Off public release validation passed.
TopoEdit-Off reports observed-positive recovery and validation-priority behavior.
The resource does not claim that:
- unlabeled candidates are experimentally validated negatives;
- ranking scores are calibrated off-target probabilities;
- validation-priority panels are wet-validated panels;
- TOPO-seq or base-editor off-target biology is universally high-mismatch in every setting.
The intended use is benchmark analysis, source-aware comparison, and prioritization of candidate panels for future experimental validation.
This GitHub repository does not include raw SRA data, genome files, alignment outputs, BAM files, FASTQ files, or large candidate-level derived tables.
Large derived tables should be archived separately as Zenodo Dataset records when they are cited directly in the manuscript.
Cite the archived Zenodo release: DOI 10.5281/zenodo.20154047. See CITATION.cff for citation metadata.
MIT.
v1.1.1