Evaluation

JAFFAL on simulated long-read fusions (Dorney et al. 2026)

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Evaluation results

1 evaluation · 40 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: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.241 F1 (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'F1'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	111 False positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'False_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.387 Precision (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'Precision'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.175 Recall (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'Recall'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	70 True positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400) 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'True_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.253 F1 (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'F1'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	165 False positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'False_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.332 Precision (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'Precision'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.205 Recall (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'Recall'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	82 True positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400) 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'True_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.291 F1 (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '95%', Algorithm 'JAFFAL', column 'F1'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	182 False positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '95%', Algorithm 'JAFFAL', column 'False_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.352 Precision (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '95%', Algorithm 'JAFFAL', column 'Precision'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.247 Recall (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '95%', Algorithm 'JAFFAL', column 'Recall'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	99 True positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400) 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '100GB', Sequence_Identity '95%', Algorithm 'JAFFAL', column 'True_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.0771 F1 (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'F1'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	27 False positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'False_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.386 Precision (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'Precision'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.0428 Recall (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'Recall'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	17 True positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397) 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '85%', Algorithm 'JAFFAL', column 'True_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.15 F1 (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'F1'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	57 False positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'False_Point'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.394 Precision (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'Precision'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	0.0925 Recall (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) fraction · 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'Recall'
Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)	Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026) Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	37 True positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400) 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 simulated long-read fusions (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-simulated-fusions 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 · stat_summary.tsv, row depth '10GB', Sequence_Identity '90%', Algorithm 'JAFFAL', column 'True_Point'

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

Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026)

Configuration: JAFFAL JAFFA 2.3 (Dorney et al. 2026)
Protocol: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026)
Dataset: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: rna-fusion-longread-20261011-protocol-simulated-fusions
dataset version: Not reported
split: Simulation
population: 400 simulated fusions per scenario
inputs: Simulated ONT reads aligned with minimap2
adaptation: Not reported
metric implementation: Partner-gene match; partial recalls counted as false positives; at least two supporting reads
aggregation: One run per scenario
budget: Not reported

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

Reproduction

Split: Simulation
Adaptation: Not reported
Scoring implementation: Partner-gene match; partial recalls counted as false positives; at least two supporting reads

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Evidence table

Inspect claims, sources and review details

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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 ↗ stat_summary.tsv, rows 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 ↗ stat_summary.tsv, rows 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 scenario Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ stat_summary.tsv, rows 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 scenario Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ stat_summary.tsv, rows 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 ↗ stat_summary.tsv, rows 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 ↗ stat_summary.tsv, rows 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 ↗ stat_summary.tsv, rows 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 ↗ stat_summary.tsv, rows 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 Simulated ONT reads aligned with minimap2 Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ stat_summary.tsv, rows 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 Simulated ONT reads aligned with minimap2 Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ stat_summary.tsv, rows 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-simulated-fusions

areas: rna-transcriptomes
contexts: clinical_research
origin: independent_paper
protocol: rna-fusion-longread-20261011-protocol-simulated-fusions
version: Primary source as retrieved 2026-10-11
comparison: protocol id: rna-fusion-longread-20261011-protocol-simulated-fusions; dataset version: Not reported; split: Simulation; population: 400 simulated fusions per scenario; inputs: Simulated ONT reads aligned with minimap2; adaptation: Not reported; metric implementation: Partner-gene match; partial recalls counted as false positives; at least two supporting reads; aggregation: One run per scenario; budget: Not reported
source locator: stat_summary.tsv, rows 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: Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026)
data: Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)
evaluation: JAFFAL simulated 100GB 85% f1-score
evaluation: JAFFAL simulated 100GB 85% false-positive-count
evaluation: JAFFAL simulated 100GB 85% precision
evaluation: JAFFAL simulated 100GB 85% recall
evaluation: JAFFAL simulated 100GB 85% true-positive-count
evaluation: JAFFAL simulated 100GB 90% f1-score
evaluation: JAFFAL simulated 100GB 90% false-positive-count
evaluation: JAFFAL simulated 100GB 90% precision
evaluation: JAFFAL simulated 100GB 90% recall
evaluation: JAFFAL simulated 100GB 90% true-positive-count
evaluation: JAFFAL simulated 100GB 95% f1-score
evaluation: JAFFAL simulated 100GB 95% false-positive-count
evaluation: JAFFAL simulated 100GB 95% precision
evaluation: JAFFAL simulated 100GB 95% recall
evaluation: JAFFAL simulated 100GB 95% true-positive-count
evaluation: JAFFAL simulated 10GB 85% f1-score
evaluation: JAFFAL simulated 10GB 85% false-positive-count
evaluation: JAFFAL simulated 10GB 85% precision
evaluation: JAFFAL simulated 10GB 85% recall
evaluation: JAFFAL simulated 10GB 85% true-positive-count
evaluation: JAFFAL simulated 10GB 90% f1-score
evaluation: JAFFAL simulated 10GB 90% false-positive-count
evaluation: JAFFAL simulated 10GB 90% precision
evaluation: JAFFAL simulated 10GB 90% recall
evaluation: JAFFAL simulated 10GB 90% true-positive-count
evaluation: JAFFAL simulated 10GB 95% f1-score
evaluation: JAFFAL simulated 10GB 95% false-positive-count
evaluation: JAFFAL simulated 10GB 95% precision
evaluation: JAFFAL simulated 10GB 95% recall
evaluation: JAFFAL simulated 10GB 95% true-positive-count
evaluation: JAFFAL simulated 1GB 90% f1-score
evaluation: JAFFAL simulated 1GB 90% false-positive-count
evaluation: JAFFAL simulated 1GB 90% precision
evaluation: JAFFAL simulated 1GB 90% recall
evaluation: JAFFAL simulated 1GB 90% true-positive-count
evaluation: JAFFAL simulated 1GB 95% f1-score
evaluation: JAFFAL simulated 1GB 95% false-positive-count
evaluation: JAFFAL simulated 1GB 95% precision
evaluation: JAFFAL simulated 1GB 95% recall
evaluation: JAFFAL simulated 1GB 95% true-positive-count

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