Dataset

Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)

New sequencing of Huh7 with two biological replicates per ONT library type, plus PacBio Kinnex and matched Illumina 150-bp paired-end RNA-seq.

Evaluation results

3 evaluations · 3 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: Union of JAFFA-direct, Arriba and STAR-Fusion on Illumina (Dorney et al. 2026)	Protocol: Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026) Dataset: Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)	15 True positives (known Huh7 fusions recovered of 34, union of callers) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Union of JAFFA-direct, Arriba and STAR-Fusion on Huh7 Illumina (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-huh7-known-fusions Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'Illumina recovered 15'
Configuration: Union of six long-read callers on ONT PCR-cDNA (Dorney et al. 2026)	Protocol: Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026) Dataset: Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)	17 True positives (known Huh7 fusions recovered of 34, union of callers) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Union of six long-read callers on Huh7 ONT PCR-cDNA (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-huh7-known-fusions Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'ONT PCR-cDNA ... (17)'
Configuration: Union of six long-read callers on PacBio Kinnex (Dorney et al. 2026)	Protocol: Huh7 recovery of 34 previously reported fusions by library type, union of callers (Dorney et al. 2026) Dataset: Huh7 hepatocellular carcinoma cell line RNA-seq: ONT direct RNA, direct cDNA, PCR-cDNA, PacBio Kinnex and Illumina NovaSeq (Dorney et al. 2026)	20 True positives (known Huh7 fusions recovered of 34, union of callers) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Union of six long-read callers on Huh7 PacBio Kinnex (Dorney et al. 2026) rna-fusion-longread-20261011-protocol-huh7-known-fusions Aggregation: Not reported A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing; LRFusionBenchmark repository (Dorney et al.): result tables and run scripts · Results 'PCR-cDNA libraries provide the most consistent recovery of validated fusion transcripts' paragraph 2: 'PacBio Kinnex ... (20)'

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

Research readiness

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

Readiness checks, gaps and artifacts

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

Evidence incomplete

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

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Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
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Dataset and evaluation context

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Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

12 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Assay ONT R10.4 cDNA and RNA004 direct RNA (MinION), PacBio Kinnex (IsoSeq3 cluster2), Illumina NovaSeq 150-bp paired-end Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay ONT R10.4 cDNA and RNA004 direct RNA (MinION), PacBio Kinnex (IsoSeq3 cluster2), Illumina NovaSeq 150-bp paired-end Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Population One cancer cell line; five library types; two replicates each Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population One cancer cell line; five library types; two replicates each Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Source location Methods 'Library preparation and RNA sequencing', 'Read processing' Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 'Library preparation and RNA sequencing', 'Read processing' Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Split Evaluation only Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split Evaluation only Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact
Description New sequencing of Huh7 with two biological replicates per ONT library type, plus PacBio Kinnex and matched Illumina 150-bp paired-end RNA-seq. Context-only references	A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv preprint version 1, posted 2026-08-12; JATS XML Retrieved: 2026-10-11T21:36:20Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description New sequencing of Huh7 with two biological replicates per ONT library type, plus PacBio Kinnex and matched Illumina 150-bp paired-end RNA-seq. Context-only references	LRFusionBenchmark repository (Dorney et al.): result tables and run scripts Original source ↗ Methods 'Library preparation and RNA sequencing', 'Read processing' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 83e629fed3098881079fd9ac1c8bc13478ce69ed (pushed 2026-08-25); files: Figures/Input_dataframes/stat_summary.tsv, Figures/Input_dataframes/counts_SGNex_summary.tsv.gz, Fusions/runtools/Run_GFSLGF.sh, Fusions/runtools/RunJAFFAL.sh, Fusions/runtools/RunCTAT-LR-fusion.sh, Fusions/runtools/RunGFSeeker.sh, SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R, CellLineData/SGNex_DiscoveryNRecall.R Retrieved: 2026-10-11T21:48:03Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `c2fa853553979a11b8cb665cf3d195cbe64530c755054f5768d05ab6ba46d17e` Hash scope: SHA-256 of a JSON bundle listing each retrieved file with its path, its own SHA-256 and its content (gzipped files decompressed); archived as artifacts/lrfusionbenchmark-bundle.json.gz Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

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

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Technical metadata and extraction receipts

Stable ID: rna-fusion-longread-20261011-data-huh7

areas: rna-transcriptomes
contexts: clinical_research
population: One cancer cell line; five library types; two replicates each
assay: ONT R10.4 cDNA and RNA004 direct RNA (MinION), PacBio Kinnex (IsoSeq3 cluster2), Illumina NovaSeq 150-bp paired-end
split: Evaluation only
source locator: Methods 'Library preparation and RNA sequencing', 'Read processing'
missing metadata: accession: reason: unavailable; note: Data availability statement gives the GEO/SRA accession as 'XXXXXXXXX'; version: reason: inapplicable

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