Configuration

Genion v1.1.0 (Dorney et al. 2026)

Genion v1.1.0: minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110).

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

3 evaluations · 93 results. Different protocols are not a single leaderboard.

Sorted by True positives (direct-cDNA library, 1Gb depth, known fusions) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	True positives (direct-cDNA library, 1Gb depth, known fusions)	True positives (direct-cDNA library, 2.5Gb depth, known fusions)	True positives (direct-cDNA library, 5Gb depth, known fusions)	True positives (direct-cDNA library, Total depth, known fusions)	True positives (direct-RNA library, 1Gb depth, known fusions)	True positives (direct-RNA library, 2.5Gb depth, known fusions)	True positives (direct-RNA library, Total depth, known fusions)	True positives (PCR-cDNA library, 10Gb depth, known fusions)	True positives (PCR-cDNA library, 1Gb depth, known fusions)	True positives (PCR-cDNA library, 2.5Gb depth, known fusions)	True positives (PCR-cDNA library, 5Gb depth, known fusions)	True positives (PCR-cDNA library, 7.5Gb depth, known fusions)	True positives (PCR-cDNA library, Total depth, known fusions)	F1 (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	F1 (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	F1 (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	F1 (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	F1 (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	F1 (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	F1 (simulated fusions, 1GB depth, 85% mean read identity, denominator 187)	False positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	False positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	False positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	False positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	False positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	False positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	False positives (simulated fusions, 1GB depth, 85% mean read identity, denominator 187)	Precision (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	Precision (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	Precision (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	Precision (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	Precision (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	Precision (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	Precision (simulated fusions, 1GB depth, 85% mean read identity, denominator 187)	Recall (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	Recall (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	Recall (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	Recall (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	Recall (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	Recall (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	Recall (simulated fusions, 1GB depth, 85% mean read identity, denominator 187)	True positives (direct-cDNA library, 7.5Gb depth, known fusions)	True positives (direct-RNA library, 5Gb depth, known fusions)	True positives (direct-RNA library, 7.5Gb depth, known fusions)	True positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	True positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	True positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	True positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	True positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	True positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	True positives (simulated fusions, 1GB depth, 85% mean read identity, denominator 187)	Count (direct-cDNA library, 1Gb depth, calls not on the known list)	Count (direct-cDNA library, 2.5Gb depth, calls not on the known list)	Count (direct-cDNA library, 5Gb depth, calls not on the known list)	Count (direct-cDNA library, Total depth, calls not on the known list)	Count (direct-RNA library, 1Gb depth, calls not on the known list)	Count (direct-RNA library, 2.5Gb depth, calls not on the known list)	Count (direct-RNA library, Total depth, calls not on the known list)	Count (PCR-cDNA library, 10Gb depth, calls not on the known list)	Count (PCR-cDNA library, 1Gb depth, calls not on the known list)	Count (PCR-cDNA library, 2.5Gb depth, calls not on the known list)	Count (PCR-cDNA library, 5Gb depth, calls not on the known list)	Count (PCR-cDNA library, 7.5Gb depth, calls not on the known list)	Count (PCR-cDNA library, Total depth, calls not on the known list)	Count (direct-cDNA library, 7.5Gb depth, calls not on the known list)	Count (direct-RNA library, 5Gb depth, calls not on the known list)	Count (direct-RNA library, 7.5Gb depth, calls not on the known list)
Genion v1.1.0 (Dorney et al. 2026)Evaluation	MCF7 ONT long-read RNA-seq, recovery of 53 known fusions and count of other calls (Dorney et al. 2026), SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 (best in column)	3 (best in column)	4 (best in column)	6 (best in column)	3 (best in column)	4 (best in column)	8 (best in column)	5 (best in column)	1 (best in column)	3 (best in column)	4 (best in column)	5 (best in column)	5 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	5	6	8	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	16	37	75	116	11	39	109	71	11	21	49	68	71	105	73	107
Genion v1.1.0 (Dorney et al. 2026)Evaluation	K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026), SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0	0	0	0	0	0	0	0	0	0	1	0	1	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	15	45	91	126	14	41	63	132	16	37	62	100	165	Not reported	Not reported	Not reported
Genion v1.1.0 (Dorney et al. 2026)Evaluation	Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026), Badread simulated ONT transcriptomes with 400 Fusim fusion transcripts (Dorney et al. 2026)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.143	0.17	0.2	0.0098	0.0194	0.0243	NA	196	225	202	9	8	7	1	0.19	0.205	0.249	0.182	0.333	0.417	0	0.115	0.145	0.168	0.00504	0.01	0.0125	0	Not reported	Not reported	Not reported	46	58	67	2	4	5	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 93 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-cDNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_1G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	15 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_1G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_2.5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	45 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_2.5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	91 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_replicate_combined', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	126 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directcDNA_replicate_combined', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-RNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_1G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	14 Count (direct-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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_1G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-RNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_2.5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	41 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_2.5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (direct-RNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_replicate_combined', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	63 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_directRNA_replicate_combined', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_10G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	132 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_10G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 1Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_1G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	16 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_1G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 2.5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_2.5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	37 Count (PCR-cDNA library, 2.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_2.5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	1 True positives (PCR-cDNA library, 5Gb depth, known fusions) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	62 Count (PCR-cDNA library, 5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	0 True positives (PCR-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_7.5G_rasusa', Algorithm 'Genion', column 'knownnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	100 Count (PCR-cDNA library, 7.5Gb depth, calls not on the known list) count · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_PCRcDNA_combined_7.5G_rasusa', Algorithm 'Genion', column 'novelnumber'
Configuration: Genion v1.1.0 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	1 True positives (PCR-cDNA library, 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 Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-sgnex-k562 Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · counts_SGNex_summary.tsv.gz, row Source 'SGNex_K562_cDNA_combined', Algorithm 'Genion', column 'knownnumber'

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A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing · Original source · bioRxiv preprint version 1, posted 2026-08-12; JATS XML
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Original source · Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R

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

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Genion
foundation model eligible: false
parameters: minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110); calls with at least two supporting reads retained
access reuse: Public open-source software
source locator: Methods 'Reference genomes', 'Fusion caller configuration'; repository Fusions/runtools/Run_GFSLGF.sh header (caller versions, min_read_supp=2)
version: v1.1.0
provenance note: Genion as run in the cited long-read fusion benchmark.

Related records

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

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