Configuration

JAFFAL JAFFA 2.3 (Dorney et al. 2026)

JAFFAL JAFFA 2.3: minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110); read-through retention enabled.

3 evaluations · 98 results

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 · 98 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, 10Gb 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, 7.5Gb 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, 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, 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, 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, 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 (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, 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, 10Gb 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, 7.5Gb 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)
JAFFAL JAFFA 2.3 (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	14 (best in column)	18 (best in column)	23 (best in column)	27 (best in column)	11 (best in column)	16 (best in column)	24 (best in column)	19 (best in column)	8 (best in column)	13 (best in column)	15 (best in column)	19 (best in column)	19 (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	26	21	24	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	4	14	29	51	4	11	28	38	5	11	25	37	38	45	17	28
JAFFAL JAFFA 2.3 (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	0	2	2	2	0	2	2	2	0	0	1	2	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	1	7	14	26	4	5	6	31	3	8	12	18	39	Not reported	Not reported	Not reported
JAFFAL JAFFA 2.3 (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	Not reported	Not reported	0.241	0.253	0.291	0.0771	0.15	0.21	0.00976	0.0372	111	165	182	27	57	87	2	3	0.387	0.332	0.352	0.386	0.394	0.396	0.333	0.571	0.175	0.205	0.247	0.0428	0.0925	0.142	0.00495	0.0192	Not reported	Not reported	Not reported	70	82	99	17	37	57	1	4	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 98 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-cDNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	1 Count (direct-cDNA library, 1Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (direct-cDNA library, 2.5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	7 Count (direct-cDNA library, 2.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (direct-cDNA library, 5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	14 Count (direct-cDNA library, 5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (direct-cDNA library, Total depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_replicate_combined', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	26 Count (direct-cDNA library, Total depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_replicate_combined', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-RNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	4 Count (direct-RNA library, 1Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (direct-RNA library, 2.5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	5 Count (direct-RNA library, 2.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (direct-RNA library, Total depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_replicate_combined', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	6 Count (direct-RNA library, Total depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_replicate_combined', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (PCR-cDNA library, 10Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_10G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	31 Count (PCR-cDNA library, 10Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_10G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	3 Count (PCR-cDNA library, 1Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 2.5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	8 Count (PCR-cDNA library, 2.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	1 True positives (PCR-cDNA library, 5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	12 Count (PCR-cDNA library, 5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (PCR-cDNA library, 7.5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_7.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	18 Count (PCR-cDNA library, 7.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_7.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 True positives (PCR-cDNA library, Total depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_cDNA_combined', Algorithm 'JAFFAL', column 'knownnumber'

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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

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Stable ID: rna-fusion-longread-20261011-config-jaffal

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: JAFFAL
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; read-through retention enabled
access reuse: Public open-source software
source locator: Methods 'Reference genomes', 'Fusion caller configuration'; repository Fusions/runtools/RunJAFFAL.sh
version: JAFFA 2.3
provenance note: JAFFAL as run in the cited long-read fusion benchmark.

Related records

configuration of: JAFFA
system: JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
system: JAFFAL on SG-NEx MCF7 ONT RNA-seq (Dorney et al. 2026)
system: JAFFAL on simulated long-read fusions (Dorney et al. 2026)

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