Evaluation

JAFFAL on SG-NEx MCF7 ONT RNA-seq (Dorney et al. 2026)

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Evaluation results

1 evaluation · 32 results. Different protocols are not a single leaderboard.

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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: MCF7 ONT long-read RNA-seq, recovery of 53 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 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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-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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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, 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	23 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	29 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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 True positives (direct-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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_7.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	45 Count (direct-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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_7.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	27 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_concatenated', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	51 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directcDNA_concatenated', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	11 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	16 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	11 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_2.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	21 True positives (direct-RNA 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	17 Count (direct-RNA 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	24 True positives (direct-RNA 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_7.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	28 Count (direct-RNA 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_7.5G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	24 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_replicate_concatenated', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	28 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_directRNA_replicate_concatenated', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	19 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_PCRcDNA_combined_10G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	38 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_PCRcDNA_combined_10G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_PCRcDNA_combined_1G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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 (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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_PCRcDNA_combined_1G_rasusa', Algorithm 'JAFFAL', column 'novelnumber'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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	13 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 MCF7 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-mcf7 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_MCF7_PCRcDNA_combined_2.5G_rasusa', Algorithm 'JAFFAL', column 'knownnumber'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026)

Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)
Protocol: MCF7 ONT long-read RNA-seq, recovery of 53 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

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: rna-fusion-longread-20261011-protocol-sgnex-mcf7
dataset version: Not reported
split: Evaluation only
population: MCF7 cell line
inputs: ONT long reads aligned with minimap2
adaptation: Not reported
metric implementation: Distinct calls matching the known list
aggregation: One run per library and depth
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Evaluation only
Adaptation: Not reported
Scoring implementation: Distinct calls matching the known list

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

36 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Not reported Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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 Retrieved: 2026-10-11T21:48:03Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison: aggregation One run per library and depth Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation One run per library and depth Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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 Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison: budget Not reported Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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 Retrieved: 2026-10-11T21:48:03Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison: dataset version Not reported Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Not reported Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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 Retrieved: 2026-10-11T21:48:03Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Comparison: inputs ONT long reads aligned with minimap2 Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs ONT long reads aligned with minimap2 Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 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 Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact

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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

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Technical metadata and extraction receipts

Stable ID: rna-fusion-longread-20261011-eval-jaffal-sgnex-mcf7

areas: rna-transcriptomes
contexts: clinical_research
origin: independent_paper
protocol: rna-fusion-longread-20261011-protocol-sgnex-mcf7
version: Primary source as retrieved 2026-10-11
comparison: protocol id: rna-fusion-longread-20261011-protocol-sgnex-mcf7; dataset version: Not reported; split: Evaluation only; population: MCF7 cell line; inputs: ONT long reads aligned with minimap2; adaptation: Not reported; metric implementation: Distinct calls matching the known list; aggregation: One run per library and depth; budget: Not reported
source locator: counts_SGNex_summary.tsv.gz, rows Cell_Lines 'MCF7', Algorithm 'JAFFAL'
missing metadata: comparison.adaptation: reason: inapplicable; note: No training; comparison.budget: reason: unreported; comparison.dataset version: reason: unreported

Related records

system: JAFFAL JAFFA 2.3 (Dorney et al. 2026)
assessment: MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026)
data: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled
evaluation: JAFFAL MCF7 direct-cDNA 1Gb knownnumber
evaluation: JAFFAL MCF7 direct-cDNA 1Gb novelnumber
evaluation: JAFFAL MCF7 direct-cDNA 2.5Gb knownnumber
evaluation: JAFFAL MCF7 direct-cDNA 2.5Gb novelnumber
evaluation: JAFFAL MCF7 direct-cDNA 5Gb knownnumber
evaluation: JAFFAL MCF7 direct-cDNA 5Gb novelnumber
evaluation: JAFFAL MCF7 direct-cDNA 7.5Gb knownnumber
evaluation: JAFFAL MCF7 direct-cDNA 7.5Gb novelnumber
evaluation: JAFFAL MCF7 direct-cDNA Total knownnumber
evaluation: JAFFAL MCF7 direct-cDNA Total novelnumber
evaluation: JAFFAL MCF7 direct-RNA 1Gb knownnumber
evaluation: JAFFAL MCF7 direct-RNA 1Gb novelnumber
evaluation: JAFFAL MCF7 direct-RNA 2.5Gb knownnumber
evaluation: JAFFAL MCF7 direct-RNA 2.5Gb novelnumber
evaluation: JAFFAL MCF7 direct-RNA 5Gb knownnumber
evaluation: JAFFAL MCF7 direct-RNA 5Gb novelnumber
evaluation: JAFFAL MCF7 direct-RNA 7.5Gb knownnumber
evaluation: JAFFAL MCF7 direct-RNA 7.5Gb novelnumber
evaluation: JAFFAL MCF7 direct-RNA Total knownnumber
evaluation: JAFFAL MCF7 direct-RNA Total novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA 10Gb knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA 10Gb novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA 1Gb knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA 1Gb novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA 2.5Gb knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA 2.5Gb novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA 5Gb knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA 5Gb novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA 7.5Gb knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA 7.5Gb novelnumber
evaluation: JAFFAL MCF7 PCR-cDNA Total knownnumber
evaluation: JAFFAL MCF7 PCR-cDNA Total novelnumber

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