Configuration

JAFFAL on nanopore cDNA reads (Lin et al. 2026)

JAFFAL as run in the cited comparison.

Overview

JAFFAL as run in the cited comparison.

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Evaluations and results

2 evaluations · 8 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: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, high-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 3) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.78 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, high-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-high-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 3, row 'JAFFAL', column 'F1'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, high-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 3) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.79 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, high-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-high-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 3, row 'JAFFAL', column 'Precision'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, high-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 3) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.76 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, high-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-high-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 3, row 'JAFFAL', column 'Sensitivity (recall)'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, high-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 3) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.81 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, high-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-high-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 3, row 'JAFFAL', column 'Specificity'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, low-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 6) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.36 f1-score fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, low-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-low-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 6, row 'JAFFAL', column 'F1'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, low-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 6) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.9 precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, low-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-low-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 6, row 'JAFFAL', column 'Precision'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, low-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 6) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.23 recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, low-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-low-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 6, row 'JAFFAL', column 'Sensitivity (recall)'
Configuration: JAFFAL on nanopore cDNA reads (Lin et al. 2026)	Protocol: Paediatric B-ALL nanopore WTS, low-depth cohort, dominant-fusion classification (Lin et al. 2026 Table 6) Dataset: Paediatric B-ALL nanopore PCR-cDNA whole-transcriptome sequencing (UNC, St Jude, ECOG-ACRIN)	0.95 specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source JAFFAL on paediatric B-ALL nanopore WTS, low-depth (Lin et al. 2026) rna-fusion-20261009-protocol-lin2026-low-depth Aggregation: Not reported Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Table 6, row 'JAFFAL', column 'Specificity'

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Release 2026-10-10-7b8f80935f90 · Record review: source checked

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Long-Read Whole-Transcriptome Sequencing and Selective Gene Panel Profiling Enable Sensitive Detection of Fusion Oncogenes in Pediatric B-Cell Acute Lymphoblastic Leukemia · Original source · Journal of Molecular Diagnostics 28(5):406, published 2026-02-10; PMC13197905 full-text XML

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Technical metadata and extraction receipts

Stable ID: rna-fusion-20261009-config-lin2026-jaffal

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: JAFFAL
foundation model eligible: false
protocol: docker://davidsongroup/jaffa:latest via apptainer, all confidence levels kept, local reformat qin=33
source locator: Materials and Methods 'JAFFAL' and 'Data Preprocessing'
missing metadata: version: reason: unreported; note: No release number printed; installation source and access dates only

Related records

configuration of: JAFFA
system: JAFFAL on paediatric B-ALL nanopore WTS, high-depth (Lin et al. 2026)
system: JAFFAL on paediatric B-ALL nanopore WTS, low-depth (Lin et al. 2026)

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