Configuration
CTAT-LR-Fusion (Dorney et al. 2026)
Configuration of CTAT-LR-Fusion: minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110).
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
3 evaluations · 99 results. Different protocols are not a single leaderboard.
Sorted by True positives (direct-cDNA library, 1Gb depth, known fusions) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | True positives (direct-cDNA library, 1Gb depth, known fusions) | True positives (direct-cDNA library, 2.5Gb depth, known fusions) | True positives (direct-cDNA library, 5Gb depth, known fusions) | True positives (direct-cDNA library, Total depth, known fusions) | True positives (direct-RNA library, 1Gb depth, known fusions) | True positives (direct-RNA library, 2.5Gb depth, known fusions) | True positives (direct-RNA library, Total depth, known fusions) | True positives (PCR-cDNA library, 1Gb depth, known fusions) | True positives (PCR-cDNA library, 2.5Gb depth, known fusions) | True positives (PCR-cDNA library, 5Gb depth, known fusions) | True positives (PCR-cDNA library, Total depth, known fusions) | F1 (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) | F1 (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) | F1 (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) | F1 (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) | F1 (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) | F1 (simulated fusions, 10GB depth, 95% mean read identity, denominator 400) | F1 (simulated fusions, 1GB depth, 85% mean read identity, denominator 187) | F1 (simulated fusions, 1GB depth, 90% mean read identity, denominator 202) | F1 (simulated fusions, 1GB depth, 95% mean read identity, denominator 208) | False positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) | False positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) | False positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) | False positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) | False positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) | False positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400) | False positives (simulated fusions, 1GB depth, 85% mean read identity, denominator 187) | False positives (simulated fusions, 1GB depth, 90% mean read identity, denominator 202) | False positives (simulated fusions, 1GB depth, 95% mean read identity, denominator 208) | Precision (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) | Precision (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) | Precision (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) | Precision (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) | Precision (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) | Precision (simulated fusions, 10GB depth, 95% mean read identity, denominator 400) | Precision (simulated fusions, 1GB depth, 85% mean read identity, denominator 187) | Precision (simulated fusions, 1GB depth, 90% mean read identity, denominator 202) | Precision (simulated fusions, 1GB depth, 95% mean read identity, denominator 208) | Recall (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) | Recall (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) | Recall (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) | Recall (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) | Recall (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) | Recall (simulated fusions, 10GB depth, 95% mean read identity, denominator 400) | Recall (simulated fusions, 1GB depth, 85% mean read identity, denominator 187) | Recall (simulated fusions, 1GB depth, 90% mean read identity, denominator 202) | Recall (simulated fusions, 1GB depth, 95% mean read identity, denominator 208) | True positives (direct-cDNA library, 7.5Gb depth, known fusions) | True positives (direct-RNA library, 5Gb depth, known fusions) | True positives (direct-RNA library, 7.5Gb depth, known fusions) | True positives (PCR-cDNA library, 10Gb depth, known fusions) | True positives (PCR-cDNA library, 7.5Gb depth, known fusions) | True positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) | True positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) | True positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) | True positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) | True positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) | True positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400) | True positives (simulated fusions, 1GB depth, 85% mean read identity, denominator 187) | True positives (simulated fusions, 1GB depth, 90% mean read identity, denominator 202) | True positives (simulated fusions, 1GB depth, 95% mean read identity, denominator 208) | Count (direct-cDNA library, 1Gb depth, calls not on the known list) | Count (direct-cDNA library, 2.5Gb depth, calls not on the known list) | Count (direct-cDNA library, 5Gb depth, calls not on the known list) | Count (direct-cDNA library, Total depth, calls not on the known list) | Count (direct-RNA library, 1Gb depth, calls not on the known list) | Count (direct-RNA library, 2.5Gb depth, calls not on the known list) | Count (direct-RNA library, Total depth, calls not on the known list) | Count (PCR-cDNA library, 1Gb depth, calls not on the known list) | Count (PCR-cDNA library, 2.5Gb depth, calls not on the known list) | Count (PCR-cDNA library, 5Gb depth, calls not on the known list) | Count (PCR-cDNA library, Total depth, calls not on the known list) | Count (direct-cDNA library, 7.5Gb depth, calls not on the known list) | Count (direct-RNA library, 5Gb depth, calls not on the known list) | Count (direct-RNA library, 7.5Gb depth, calls not on the known list) | Count (PCR-cDNA library, 10Gb depth, calls not on the known list) | Count (PCR-cDNA library, 7.5Gb depth, calls not on the known list) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTAT-LR-Fusion (Dorney et al. 2026)Evaluation | MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026), SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled | 15 (best in column) | 20 (best in column) | 23 (best in column) | 27 (best in column) | 12 (best in column) | 17 (best in column) | 25 (best in column) | 11 (best in column) | 14 (best in column) | 17 (best in column) | 20 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 26 | 21 | 25 | 20 | 20 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 74 | 196 | 352 | 563 | 7 | 17 | 36 | 4 | 18 | 36 | 51 | 535 | 29 | 36 | 51 | 47 |
| CTAT-LR-Fusion (Dorney et al. 2026)Evaluation | K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026), SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 0 | 1 | 1 | 2 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 86 | 225 | 437 | 577 | 8 | 15 | 10 | 6 | 15 | 23 | 23 | Not reported | Not reported | Not reported | Not reported | Not reported |
| CTAT-LR-Fusion (Dorney et al. 2026)Evaluation | Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026), Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.205 | 0.292 | 0.349 | 0.141 | 0.278 | 0.306 | NA | NA | 0.0188 | 72 | 109 | 134 | 51 | 70 | 98 | 2 | 1 | 3 | 0.429 | 0.444 | 0.457 | 0.4 | 0.521 | 0.479 | 0 | 0 | 0.4 | 0.135 | 0.217 | 0.282 | 0.0856 | 0.19 | 0.225 | 0 | 0 | 0.00962 | Not reported | Not reported | Not reported | Not reported | Not reported | 54 | 87 | 113 | 34 | 76 | 90 | 0 | 0 | 2 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 99 result rows with coverage, uncertainty and sources
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing · Original source · bioRxiv preprint version 1, posted 2026-08-12; JATS XML
- LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Original source · Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R
Technical metadata and extraction receipts
Stable ID: rna-fusion-longread-20261011-config-ctat-lr-fusion
- areas
- rna-transcriptomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- CTAT-LR-Fusion
- foundation model eligible
- false
- parameters
- minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110); calls with at least two supporting reads retained
- access reuse
- Public open-source software
- source locator
- Methods 'Reference genomes', 'Fusion caller configuration'; repository Fusions/runtools/RunCTAT-LR-fusion.sh header
- missing metadata
- version: reason: unreported; note: Not printed in the preprint or the pinned run scripts
- provenance note
- CTAT-LR-Fusion as run in the cited long-read fusion benchmark.