rewirebio.iobenchmarks
Evidence claim

Relevance of Simulated long-read fusion detection (Dorney et al. 2026) to "Select a tumour RNA fusion-detection workflow"

Use case
Select a tumour RNA fusion-detection workflow
Assessed by
Simulated long-read fusion detection, 400 fusions at three depths and three read identities (Dorney et al. 2026)
Relevance
Proxy evidence
Endpoint
Precision, recall, F1 and true and false call counts of six long-read fusion callers on 400 simulated fusions at nine depth and read-identity scenarios

Proxy, not direct: an independent comparison of long-read callers with a complete truth set measures sensitivity and false calls, but the reads and fusions are simulated, not tumour RNA.

6 reviewed evaluations

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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

38 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Citation locations
2 values
  • source id
    rna-fusion-longread-20261011-source-dorney2026
    locator
    Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests
  • source id
    rna-fusion-longread-20261011-source-dorney2026-repository
    locator
    Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
Context-only references
A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.citation_locators

Source artifact SHA-256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Citation locations
2 values
  • source id
    rna-fusion-longread-20261011-source-dorney2026
    locator
    Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests
  • source id
    rna-fusion-longread-20261011-source-dorney2026-repository
    locator
    Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
Context-only references
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.citation_locators

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

Comparison group
dorney2026-longread
Context-only references
A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.comparison_group

Source artifact SHA-256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison group
dorney2026-longread
Context-only references
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.comparison_group

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

Comparison title
Long-read fusion callers, independent benchmark (Dorney et al. 2026)
Context-only references
A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.comparison_title

Source artifact SHA-256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison title
Long-read fusion callers, independent benchmark (Dorney et al. 2026)
Context-only references
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.comparison_title

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

Constraints
2 values
  • Inspect every linked evaluation's source locator before citing a result.
  • Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources.
Context-only references
A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.constraints

Source artifact SHA-256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Constraints
2 values
  • Inspect every linked evaluation's source locator before citing a result.
  • Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources.
Context-only references
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.constraints

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

Endpoint
Precision, recall, F1 and true and false call counts of six long-read fusion callers on 400 simulated fusions at nine depth and read-identity scenarios
Context-only references
A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.endpoint

Source artifact SHA-256: c665bb407799324bc50ae1792d82574a41ae4a9182befd360973d89a82cbaa5b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Endpoint
Precision, recall, F1 and true and false call counts of six long-read fusion callers on 400 simulated fusions at nine depth and read-identity scenarios
Context-only references
LRFusionBenchmark repository (Dorney et al.): result tables and run scripts

Original source ↗

rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R

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.endpoint

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

How to read the evidence

Sources and history

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

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-rna-fusion-longread-20261011-simulated-fusions

field
links:assessed_by:rna-fusion-longread-20261011-protocol-simulated-fusions
value
rna-fusion-longread-20261011-protocol-simulated-fusions
relevance
proxy
endpoint
Precision, recall, F1 and true and false call counts of six long-read fusion callers on 400 simulated fusions at nine depth and read-identity scenarios
rationale
Proxy, not direct: an independent comparison of long-read callers with a complete truth set measures sensitivity and false calls, but the reads and fusions are simulated, not tumour RNA.
constraints
Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; truth sets, specimens, sequencing and caller versions differ between sources.
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.; Simulated reads with synthetic fusions, not tumour RNA; most simulated fusions are not cancer drivers.; At 1 Gb the denominator (Spiked_Number) is 187 to 208 rather than 400, and at 10 Gb and 85% identity it is 397; the source does not explain why. Some callers have no row at 1 Gb (no calls).; Results prose gives false-call counts (GFSeeker 632, FusionSeeker 519, JAFFAL 106, CTAT-LR-Fusion 38) that do not match any row of the table; the scenario or filter they refer to is not stated.; Single simulation per scenario; no interval estimates. The FDR and Sensitivity columns repeat 1 minus precision and recall and are not recorded.
citation locators
source id: rna-fusion-longread-20261011-source-dorney2026; locator: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; source id: rna-fusion-longread-20261011-source-dorney2026-repository; locator: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
source locator
rna-fusion-longread-20261011-source-dorney2026: Results; Methods 'Simulation datasets', 'Public long-read datasets', 'Benchmark evaluation criteria'; Competing interests; rna-fusion-longread-20261011-source-dorney2026-repository: Figures/Input_dataframes/stat_summary.tsv; counts_SGNex_summary.tsv.gz; SimulatedData/Data_Analysis_Scripts/Precision_Recall_ReadSupp_stats.R; CellLineData/SGNex_DiscoveryNRecall.R
headline metric
f1-score
reason
Add a relevance judgement from the 2026-10-11 oncology use-case literature pass.
comparison group
dorney2026-longread
comparison title
Long-read fusion callers, independent benchmark (Dorney et al. 2026)
stratum label
Simulated reads, 400 fusions
stratum order
1
reviewed evaluations
rna-fusion-longread-20261011-eval-ctat-lr-fusion-simulated-fusions; rna-fusion-longread-20261011-eval-fusionseeker-simulated-fusions; rna-fusion-longread-20261011-eval-genion-simulated-fusions; rna-fusion-longread-20261011-eval-gfseeker-simulated-fusions; rna-fusion-longread-20261011-eval-jaffal-simulated-fusions; rna-fusion-longread-20261011-eval-longgf-simulated-fusions
review
method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs and output, the relevance rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude research agent reviewer-onc-2, independent of the extractor uc-oncology; no human review claimed; reviewed at: 2026-10-11T23:30:00Z; note: Automated review; not human scientific review. See docs/reviews/use-cases/tumour-rna-fusion-detection-2026-10-11.md.
pins
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