Protocol

K562 ONT long-read RNA-seq, recovery of 6 known fusions and count of other calls (Dorney et al. 2026)

Per-caller number of known K562 fusions recovered and number of other (putative novel) calls, by library type and depth.

6 evaluations · 152 results

Overview

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

6 recorded evaluations, 152 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

6 evaluations · 152 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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: 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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	86 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	225 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	437 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	577 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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, 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	8 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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-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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	10 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	6 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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 (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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	23 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: CTAT-LR-Fusion (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 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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'knownnumber'
Configuration: CTAT-LR-Fusion (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	23 Count (PCR-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 CTAT-LR-Fusion 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 'CTAT-LR-Fusion', column 'novelnumber'
Configuration: FusionSeeker v1.0.1 (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 FusionSeeker 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 'FusionSeeker', column 'knownnumber'
Configuration: FusionSeeker v1.0.1 (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	610 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 FusionSeeker 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 'FusionSeeker', column 'novelnumber'
Configuration: FusionSeeker v1.0.1 (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 FusionSeeker 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 'FusionSeeker', 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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Technical metadata and extraction receipts

Stable ID: rna-fusion-longread-20261011-protocol-sgnex-k562

areas: rna-transcriptomes
contexts: clinical_research
protocol: Calls annotated against the authors' list of previously reported K562 fusions (6); knownnumber counts distinct calls labelled known and novelnumber all other distinct calls (repository CellLineData/SGNex_DiscoveryNRecall.R).
version: Repository commit 83e629fed309, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz
metric: true-positive-count
denominator: 6
limitations: Independent benchmark: the authors developed none of the six callers (Competing interests: none). Preprint, not peer reviewed.; Caller versions for CTAT-LR-Fusion and GFSeeker are not stated.; The known list (6 fusions) comes from the literature; fusions missing from it count as other calls, so the other-call count mixes real unlisted fusions and false calls.; No read-support filter is applied in the counting script; the run-level two-read filter stated in Methods may or may not apply here.; Counts only; no precision or recall printed. Single run per library and depth.; knownnumber is the number of distinct call records the authors' script labels known (grouped by gene pair, chromosomes and fusion type); the script does not deduplicate them to listed fusions, so it is an upper bound on the number of listed fusions recovered.; Only six known K562 fusions, so recovery is coarse.; CTAT-LR-Fusion has no K562 PCR-cDNA rows at 7.5 or 10 Gb, and no caller has K562 direct-RNA rows above 2.5 Gb or direct-cDNA rows above 5 Gb; the source does not say why.
source locator: Results paragraph on SG-NEx K562 and MCF7; repository counts_SGNex_summary.tsv.gz and SGNex_DiscoveryNRecall.R

Related records

uses data: SG-NEx K562 and MCF7 ONT long-read RNA-seq (PCR-cDNA, direct cDNA, direct RNA), subsampled
assessment: CTAT-LR-Fusion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessment: FusionSeeker on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessment: Genion on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessment: GFSeeker on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessment: JAFFAL on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessment: LongGF on SG-NEx K562 ONT RNA-seq (Dorney et al. 2026)
assessed by: Select a tumour RNA fusion-detection workflow

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