Configuration

LongGF v0.1.2 (Dorney et al. 2026)

LongGF v0.1.2: 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 · 98 results. Different protocols are not a single leaderboard.

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

Tested configuration	Protocol and dataset	True positives (direct-cDNA library, 1Gb depth, known fusions)	True positives (direct-cDNA library, 2.5Gb depth, known fusions)	True positives (direct-cDNA library, 5Gb depth, known fusions)	True positives (direct-cDNA library, Total depth, known fusions)	True positives (direct-RNA library, 1Gb depth, known fusions)	True positives (direct-RNA library, 2.5Gb depth, known fusions)	True positives (direct-RNA library, Total depth, known fusions)	True positives (PCR-cDNA library, 10Gb depth, known fusions)	True positives (PCR-cDNA library, 1Gb depth, known fusions)	True positives (PCR-cDNA library, 2.5Gb depth, known fusions)	True positives (PCR-cDNA library, 5Gb depth, known fusions)	True positives (PCR-cDNA library, 7.5Gb depth, known fusions)	True positives (PCR-cDNA library, Total depth, known fusions)	F1 (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	F1 (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	F1 (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	F1 (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	F1 (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	F1 (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	F1 (simulated fusions, 1GB depth, 90% mean read identity, denominator 202)	F1 (simulated fusions, 1GB depth, 95% mean read identity, denominator 208)	False positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	False positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	False positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	False positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	False positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	False positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	False positives (simulated fusions, 1GB depth, 90% mean read identity, denominator 202)	False positives (simulated fusions, 1GB depth, 95% mean read identity, denominator 208)	Precision (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	Precision (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	Precision (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	Precision (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	Precision (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	Precision (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	Precision (simulated fusions, 1GB depth, 90% mean read identity, denominator 202)	Precision (simulated fusions, 1GB depth, 95% mean read identity, denominator 208)	Recall (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	Recall (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	Recall (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	Recall (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	Recall (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	Recall (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	Recall (simulated fusions, 1GB depth, 90% mean read identity, denominator 202)	Recall (simulated fusions, 1GB depth, 95% mean read identity, denominator 208)	True positives (direct-cDNA library, 7.5Gb depth, known fusions)	True positives (direct-RNA library, 5Gb depth, known fusions)	True positives (direct-RNA library, 7.5Gb depth, known fusions)	True positives (simulated fusions, 100GB depth, 85% mean read identity, denominator 400)	True positives (simulated fusions, 100GB depth, 90% mean read identity, denominator 400)	True positives (simulated fusions, 100GB depth, 95% mean read identity, denominator 400)	True positives (simulated fusions, 10GB depth, 85% mean read identity, denominator 397)	True positives (simulated fusions, 10GB depth, 90% mean read identity, denominator 400)	True positives (simulated fusions, 10GB depth, 95% mean read identity, denominator 400)	True positives (simulated fusions, 1GB depth, 90% mean read identity, denominator 202)	True positives (simulated fusions, 1GB depth, 95% mean read identity, denominator 208)	Count (direct-cDNA library, 1Gb depth, calls not on the known list)	Count (direct-cDNA library, 2.5Gb depth, calls not on the known list)	Count (direct-cDNA library, 5Gb depth, calls not on the known list)	Count (direct-cDNA library, Total depth, calls not on the known list)	Count (direct-RNA library, 1Gb depth, calls not on the known list)	Count (direct-RNA library, 2.5Gb depth, calls not on the known list)	Count (direct-RNA library, Total depth, calls not on the known list)	Count (PCR-cDNA library, 10Gb depth, calls not on the known list)	Count (PCR-cDNA library, 1Gb depth, calls not on the known list)	Count (PCR-cDNA library, 2.5Gb depth, calls not on the known list)	Count (PCR-cDNA library, 5Gb depth, calls not on the known list)	Count (PCR-cDNA library, 7.5Gb depth, calls not on the known list)	Count (PCR-cDNA library, Total depth, calls not on the known list)	Count (direct-cDNA library, 7.5Gb depth, calls not on the known list)	Count (direct-RNA library, 5Gb depth, calls not on the known list)	Count (direct-RNA library, 7.5Gb depth, calls not on the known list)
LongGF v0.1.2 (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	3 (best in column)	7 (best in column)	11 (best in column)	14 (best in column)	5 (best in column)	7 (best in column)	10 (best in column)	7 (best in column)	3 (best in column)	3 (best in column)	6 (best in column)	7 (best in column)	7 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	13	9	10	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	33	69	122	162	14	14	29	53	7	16	32	48	53	152	23	29
LongGF v0.1.2 (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	1	1	1	1	0	1	1	1	0	1	1	1	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	Not reported	Not reported	Not reported	Not reported	Not reported	33	69	112	140	2	3	5	71	9	17	34	56	91	Not reported	Not reported	Not reported
LongGF v0.1.2 (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	0.0402	0.0431	0.0426	0.0186	0.0391	0.0437	NA	NA	88	100	106	30	51	48	1	1	0.102	0.0991	0.094	0.118	0.15	0.172	0	0	0.025	0.0275	0.0275	0.0101	0.0225	0.025	0	0	Not reported	Not reported	Not reported	10	11	11	4	9	10	0	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 98 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_1G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	33 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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_1G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	69 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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	112 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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_replicate_combined.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	140 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 LongGF 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 'LongGF.run.SGNex_K562_directcDNA_replicate_combined.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_1G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	2 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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_1G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	3 Count (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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 (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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_replicate_combined.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (Dorney et al. 2026)	Protocol: K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026) Dataset: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled	5 Count (direct-RNA library, 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 LongGF 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 'LongGF.run.SGNex_K562_directRNA_replicate_combined.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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, 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_10G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	71 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_10G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_1G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	9 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_1G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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, 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	17 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_2.5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	34 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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, 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_7.5G_rasusa.tsv', Algorithm 'LongGF', column 'knownnumber'
Configuration: LongGF v0.1.2 (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	56 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 LongGF 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 'LongGF.run.SGNex_K562_PCRcDNA_combined_7.5G_rasusa.tsv', Algorithm 'LongGF', column 'novelnumber'
Configuration: LongGF v0.1.2 (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 LongGF 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 'LongGF.run.SGNex_K562_cDNA_combined.tsv', Algorithm 'LongGF', 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-longgf

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: LongGF
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: v0.1.2
provenance note: LongGF as run in the cited long-read fusion benchmark.

Related records

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

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