Dataset

Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)

Simulated long-read RNA-seq: GENCODE transcriptome with HepG2-derived abundances plus Fusim fusions (100 each inter-chromosomal, intra-chromosomal, read-through and tri-gene; self-fusions excluded), Badread Nanopore2023 error model at 1, 10 and 100 Gb and mean identity 85%, 90% and 95%.

Evaluation results

6 evaluations · 250 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: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'F1'
Configuration: CTAT-LR-Fusion (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)	72 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'False_Point'
Configuration: CTAT-LR-Fusion (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)	0.429 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Precision'
Configuration: CTAT-LR-Fusion (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)	0.135 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Recall'
Configuration: CTAT-LR-Fusion (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)	54 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'True_Point'
Configuration: CTAT-LR-Fusion (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)	0.292 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'F1'
Configuration: CTAT-LR-Fusion (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)	109 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'False_Point'
Configuration: CTAT-LR-Fusion (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)	0.444 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Precision'
Configuration: CTAT-LR-Fusion (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)	0.217 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Recall'
Configuration: CTAT-LR-Fusion (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)	87 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'True_Point'
Configuration: CTAT-LR-Fusion (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)	0.349 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'F1'
Configuration: CTAT-LR-Fusion (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)	134 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'False_Point'
Configuration: CTAT-LR-Fusion (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)	0.457 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Precision'
Configuration: CTAT-LR-Fusion (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)	0.282 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Recall'
Configuration: CTAT-LR-Fusion (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)	113 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'True_Point'
Configuration: CTAT-LR-Fusion (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)	0.141 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'F1'
Configuration: CTAT-LR-Fusion (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)	51 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'False_Point'
Configuration: CTAT-LR-Fusion (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)	0.4 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Precision'
Configuration: CTAT-LR-Fusion (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)	0.0856 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Recall'
Configuration: CTAT-LR-Fusion (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)	34 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'True_Point'
Configuration: CTAT-LR-Fusion (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)	0.278 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'F1'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'False_Point'
Configuration: CTAT-LR-Fusion (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)	0.521 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Precision'
Configuration: CTAT-LR-Fusion (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)	0.19 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'Recall'
Configuration: CTAT-LR-Fusion (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)	76 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'True_Point'

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

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0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

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

Evidence incomplete

Replay metrics

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
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Score meaning and direction are confirmed: not yet verified
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Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

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Missing or unresolved evidence

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Verified: Not verified

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Evidence

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Evidence table

Inspect claims, sources and review details

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12 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
Assay Badread v0.4.1 simulated ONT reads, 0.1% artificial chimeras, adapters removed with Porechop ABI Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.assay` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Badread v0.4.1 simulated ONT reads, 0.1% artificial chimeras, adapters removed with Porechop ABI Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.assay` 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
Population Nine simulated scenarios; 400 scored fusions (fewer present at low depth: Spiked_Number column) Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.population` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population Nine simulated scenarios; 400 scored fusions (fewer present at low depth: Spiked_Number column) Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.population` 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
Source location Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.source_locator` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.source_locator` 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
Split Simulation only Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.split` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Simulation only Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `attributes.split` 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
Description Simulated long-read RNA-seq: GENCODE transcriptome with HepG2-derived abundances plus Fusim fusions (100 each inter-chromosomal, intra-chromosomal, read-through and tri-gene; self-fusions excluded), Badread Nanopore2023 error model at 1, 10 and 100 Gb and mean identity 85%, 90% and 95%. Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `description` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Simulated long-read RNA-seq: GENCODE transcriptome with HepG2-derived abundances plus Fusim fusions (100 each inter-chromosomal, intra-chromosomal, read-through and tri-gene; self-fusions excluded), Badread Nanopore2023 error model at 1, 10 and 100 Gb and mean identity 85%, 90% and 95%. Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number' 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 Audit details Field: `description` 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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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-data-badread-simulated-fusions

areas: rna-transcriptomes
contexts: clinical_research
population: Nine simulated scenarios; 400 scored fusions (fewer present at low depth: Spiked_Number column)
assay: Badread v0.4.1 simulated ONT reads, 0.1% artificial chimeras, adapters removed with Porechop ABI
split: Simulation only
source locator: Methods 'Simulation datasets'; repository stat_summary.tsv column 'Spiked_Number'
missing metadata: version: reason: unreported

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