Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Genome Biology · 2019 · Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML · Peer-reviewed
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- method_description: rna-fusion-20261009-method-arriba: Method description Arriba extracts gene fusions from the chimeric alignments reported by STAR [ 18 ] by applying a collection of filters which recognize frequent types of artifacts found in RNA-Seq data. (Table 1, row 'Arriba', column 'Brief overview of methodology')
- method_description: rna-fusion-20261009-method-ericscript: Method description BWA [ 26 ] is used to align reads to the genome. Discordant reads are used to identify candidate gene fusions. BLAT [ 27 ] is then used in an iterative local alignment step to define precise fusion breakpoints by aligning to customized targets of fused exons. An AdaBoost classifier trained with synthetic data is used to score and rank fusion predictions. (Table 1, row 'EricScript', column 'Brief overview of methodology')
- method_description: rna-fusion-20261009-method-star-fusion: Method description Uses chimeric read alignments reported by STAR in its Chimeric.out.junction file to identify candidate fusions followed by extensive filtering of likely artifacts. (Table 1, row 'STAR-Fusion', column 'Brief overview of methodology')
- reported_ranking: rna-fusion-20261009-method-ericscript: Reported ranking In contrast to an earlier assessment of fusion prediction accuracy that found EricScript to be top-ranking [ 16 ], in our assessment, EricScript was the least accurate method on cancer cell line RNA-seq, suffering mostly from a high rate of false positives. (Discussion paragraph 2, sentence 5)
- reported_ranking: rna-fusion-20261009-method-star-fusion: Reported ranking In particular, STAR-Fusion, Arriba, and STAR-SEQR had the best combination of speed and accuracy compared to 19 other methods evaluated on cancer transcriptome data. (Discussion paragraph 2, sentence 1)
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28 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 9828428800fb119b30742d6f6f0b1aabf4b8cd34bd889768c462ca440cd65108 Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6802306/fullTextXML Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1186/s13059-019-1842-9 Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Licence CC-BY-4.0 Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Media type application/xml Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-10-12T20:53:32Z Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.review.artifact_sha256 9828428800fb119b30742d6f6f0b1aabf4b8cd34bd889768c462ca440cd65108 Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Review: date 2026-10-12 Source metadata | Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Review method1 values
| Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods No field-specific location recorded Version: Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Primary source retrieved and hashed for the 2026-10-12 ML-versus-baseline pass.
Technical metadata and extraction receipts
Stable ID: rna-fusion-20261012-haas2019-source
- areas
- rna-transcriptomes
- contexts
- research
- url
- https://doi.org/10.1186/s13059-019-1842-9
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6802306/fullTextXML
- version
- Genome Biology 20:213, published 2019-10-21; PMC6802306 full-text XML
- retrieved at
- 2026-10-12T20:53:32Z
- artifact sha256
- 9828428800fb119b30742d6f6f0b1aabf4b8cd34bd889768c462ca440cd65108
- doi
- 10.1186/s13059-019-1842-9
- publication status
- peer_reviewed
- licence
- CC-BY-4.0
- media type
- application/xml
- venue
- Genome Biology
- year
- 2019
- source locator
- Licence statement in the article XML <license> element: Creative Commons Attribution 4.0
- scope decision
- No results extracted: per-method accuracy (P-R AUC, TPR and PPV at maximum F1, leaderboard rankings) is shown only in Figures 1b, 2a, 4a, 4c, 4d and Additional file 2 Figures S3, S5, S8 and S9. Additional file 1 holds per-fusion predictions, not accuracy values, and the FusionBenchmarking repository holds code, not result tables.
- review
- method: source-hash-verification; reviewer: claude; reviewer note: Separate Claude review agent (rev-mlvb), independent of the extracting agent; no human review claimed; date: 2026-10-12; artifact sha256: 9828428800fb119b30742d6f6f0b1aabf4b8cd34bd889768c462ca440cd65108; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6802306/fullTextXML; note: Re-downloaded the Europe PMC full-text XML and matched its SHA-256.