Configuration

GFSeeker (Dorney et al. 2026)

Configuration of GFSeeker: minimap2 2.28 alignments to hg38 with GENCODE v44 (JAFFAL: UCSC GENCODE v43; Genion: Ensembl 110).

3 evaluations · 103 results

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 · 103 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	7 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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 (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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	55 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	81 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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 (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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	22 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	31 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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, 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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	101 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	7 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	19 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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, 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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	43 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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, 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 GFSeeker 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 'GFSeeker', column 'knownnumber'
Configuration: GFSeeker (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	65 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 GFSeeker 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 'GFSeeker', column 'novelnumber'
Configuration: GFSeeker (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 GFSeeker 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 'GFSeeker', 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-gfseeker

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: GFSeeker
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/RunGFSeeker.sh
missing metadata: version: reason: unreported; note: Not printed in the preprint or the pinned run scripts
provenance note: GFSeeker as run in the cited long-read fusion benchmark.

Related records

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

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