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SQUIRLS (Smith and Kitzman 2023)

Configuration of SQUIRLS: version 1.0.0; Default settings; default hg19 Ensembl annotation.

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

6 evaluations · 22 results. Different protocols are not a single leaderboard.

Sorted by Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants)	Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants)	Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites)	Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants)
SQUIRLS (Smith and Kitzman 2023)Evaluation	WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.962 (best in column)	1 (best in column)	0.889	0.929
SQUIRLS (Smith and Kitzman 2023)Evaluation	POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.916	0.9	0.95 (best in column)	0.96 (best in column)
SQUIRLS (Smith and Kitzman 2023)Evaluation	MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.746	0.641	0.929	0.95
SQUIRLS (Smith and Kitzman 2023)Evaluation	BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.655	0.455	0.594	0.665
SQUIRLS (Smith and Kitzman 2023)Evaluation	MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.115	0.0824	0.136	0.176
SQUIRLS (Smith and Kitzman 2023)Evaluation	FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2), FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.0526	0.0526	Not reported	Not reported

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.655 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B5; row SQUIRLS, column BRCA1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.455 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B13; row Exon_SQUIRLS, column BRCA1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.665 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B21; row Intron_SQUIRLS, column BRCA1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: BRCA1 saturation genome editing, synonymous and intronic SNVs: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: BRCA1 saturation genome editing, synonymous and intronic SNVs (Smith and Kitzman benchmark set)	0.594 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on BRCA1 saturation genome editing, synonymous and intronic SNVs splicing-follow-up-20261009-protocol-smith2023-brca1-sge-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell B29; row Intron_NonCanon_SQUIRLS, column BRCA1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.0526 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell C5; row SQUIRLS, column FAS
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: FAS exon 6 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: FAS exon 6 saturation MPSA (Smith and Kitzman benchmark set)	0.0526 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on FAS exon 6 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-fas-exon6-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell C13; row Exon_SQUIRLS, column FAS
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.746 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D5; row SQUIRLS, column MLH1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.641 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D13; row Exon_SQUIRLS, column MLH1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.95 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D21; row Intron_SQUIRLS, column MLH1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MLH1 curated clinical splicing variants: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MLH1 curated clinical splicing variants (Smith and Kitzman benchmark set)	0.929 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MLH1 curated clinical splicing variants splicing-follow-up-20261009-protocol-smith2023-mlh1-curated-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell D29; row Intron_NonCanon_SQUIRLS, column MLH1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.115 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F5; row SQUIRLS, column RON
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.0824 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F13; row Exon_SQUIRLS, column RON
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.176 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F21; row Intron_SQUIRLS, column RON
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: MST1R (RON) exon 11 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: MST1R (RON) exon 11 saturation MPSA (Smith and Kitzman benchmark set)	0.136 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on MST1R (RON) exon 11 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-mst1r-exon11-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell F29; row Intron_NonCanon_SQUIRLS, column RON
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.916 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E5; row SQUIRLS, column POU1F1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.9 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E13; row Exon_SQUIRLS, column POU1F1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.96 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E21; row Intron_SQUIRLS, column POU1F1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: POU1F1 exon 2 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: POU1F1 exon 2 saturation MPSA (Smith and Kitzman benchmark set)	0.95 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on POU1F1 exon 2 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-pou1f1-exon2-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell E29; row Intron_NonCanon_SQUIRLS, column POU1F1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.962 Recall (transcriptome-normalised threshold calling 10% of background SNVs; all variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G5; row SQUIRLS, column WT1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	1 Recall (transcriptome-normalised threshold calling 10% of background SNVs; exonic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G13; row Exon_SQUIRLS, column WT1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.929 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G21; row Intron_SQUIRLS, column WT1
Configuration: SQUIRLS (Smith and Kitzman 2023)	Protocol: WT1 exon 9 saturation MPSA: transcriptome-normalised sensitivity at a 10% background call rate (Smith and Kitzman Table S2) Dataset: WT1 exon 9 saturation MPSA (Smith and Kitzman benchmark set)	0.889 Recall (transcriptome-normalised threshold calling 10% of background SNVs; intronic variants excluding essential splice sites) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source SQUIRLS on WT1 exon 9 saturation MPSA splicing-follow-up-20261009-protocol-smith2023-wt1-exon9-mpsa-tn10 Aggregation: Not reported Benchmarking splice variant prediction algorithms using massively parallel splicing assays; Smith and Kitzman 2023, Additional file 3 (Table S2) · Additional file 3 sheet 'Sensitivity 10% SDV', cell G29; row Intron_NonCanon_SQUIRLS, column WT1

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Benchmarking splice variant prediction algorithms using massively parallel splicing assays · Original source · Genome Biology 24:294, published 2023-12-21; PMC10734170 full-text XML
Smith and Kitzman 2023, Additional file 3 (Table S2) · Original source · 13059_2023_3144_MOESM3_ESM.xlsx inside the Europe PMC supplementaryFiles zip for PMC10734170

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Technical metadata and extraction receipts

Stable ID: splicing-follow-up-20261009-config-smith2023-squirls-1-0-0

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: SQUIRLS (Smith and Kitzman 2023)
foundation model eligible: false
version: 1.0.0
parameters: Default settings; default hg19 Ensembl annotation. Transcriptome-normalised threshold calling 10% of 500,000 background SNVs: 0.0112251216773705 (Table S2 'Thresholds' column C)
source locator: Methods 'Scoring with eight splice effect predictors'; Additional file 3 'Thresholds'
provenance note: SQUIRLS (Smith and Kitzman 2023) as run in the cited comparison.

Related records

configuration of: SQUIRLS
system: SQUIRLS on BRCA1 saturation genome editing, synonymous and intronic SNVs
system: SQUIRLS on FAS exon 6 saturation MPSA
system: SQUIRLS on MLH1 curated clinical splicing variants
system: SQUIRLS on MST1R (RON) exon 11 saturation MPSA
system: SQUIRLS on POU1F1 exon 2 saturation MPSA
system: SQUIRLS on WT1 exon 9 saturation MPSA

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