How ylab-hi/scanneo2 works
ScanNeo2 is a Snakemake workflow that turns RNA-sequencing and variant inputs into predicted neoantigens. Users configure and launch the workflow; documented event sources include SNVs, indels, canonical and exitron splicing, and gene fusions, with custom variants also supported. Prioritization reconstructs variant effects, predicts MHC binding, and adds immunogenicity and similarity scores. The README establishes the product workflow and source capabilities; prioritization connections are supported by excerpts, while unsampled workflow-rule connections are shown as unverified.
Main entry points: Snakefile Workflow orchestration · compile.py Prioritization entry · effects.py Variant effects · hlatyping_prep.smk HLA preparation
Components 22
Workflow stages
- Workflow configuration
config/config.yaml - Workflow orchestration
workflow/Snakefile - RNA processing
workflow/rules/preproc.smk - Read alignment
workflow/rules/align.smk - Expression quantification
workflow/rules/quantification.smk - Variant event sources
workflow/rules
HLA genotyping
- HLA preparation
workflow/rules/hlatyping_prep.smk - MHC-I typing
workflow/rules/hlatyping_mhcI.smk - MHC-II typing
workflow/rules/hlatyping_mhcII.smk
Prioritization
- Prioritization entry
workflow/scripts/prioritization/compile.py - Variant effects
workflow/scripts/prioritization/effects.py - Variant processing
workflow/scripts/prioritization/variants.py - Fusion processing
workflow/scripts/prioritization/fusions.py - Protein input processing
workflow/scripts/prioritization/proteins.py - Reference data
workflow/scripts/prioritization/reference.py - MHC binding prediction
workflow/scripts/prioritization/prediction.py - Immunogenicity and similarity
workflow/scripts/prioritization/filtering.py
Results and reporting
- Variant effects tables
workflow/scripts/prioritization/effects.py - Neoepitope tables
workflow/scripts/prioritization/prediction.py - Reporting
workflow/scripts/report.py - Summary
workflow/scripts/summarize.py
Other components
- Researcher
Connections 32
- Researcher → Workflow configuration: sets options
README.md - Researcher → Workflow orchestration: launches workflow
README.md - Workflow configuration → Workflow orchestration: configures
- Workflow orchestration → RNA processing: dispatches
- Workflow orchestration → Read alignment: dispatches
- Workflow orchestration → Expression quantification: dispatches
- Workflow orchestration → Variant event sources: dispatches
- Workflow orchestration → HLA preparation: dispatches
- Workflow orchestration → Prioritization entry: dispatches
- RNA processing → Read alignment: supplies reads
- Read alignment → Expression quantification: supplies alignments
- HLA preparation → MHC-I typing: prepares typing
- HLA preparation → MHC-II typing: prepares typing
- Variant event sources → Prioritization entry: provides event inputs
- MHC-I typing → Prioritization entry: provides alleles
- MHC-II typing → Prioritization entry: provides alleles
- Expression quantification → Prioritization entry: provides expression
- Prioritization entry → Variant processing: processes variants
workflow/scripts/prioritization/compile.py - Prioritization entry → Fusion processing: processes fusions
workflow/scripts/prioritization/compile.py - Prioritization entry → Protein input processing: processes custom proteins
workflow/scripts/prioritization/compile.py - Variant processing → Variant effects: registers effects
workflow/scripts/prioritization/variants.py - Fusion processing → Variant effects: registers effects
workflow/scripts/prioritization/fusions.py - Protein input processing → Variant effects: registers effects
workflow/scripts/prioritization/proteins.py - Variant processing → Reference data: loads annotation
workflow/scripts/prioritization/variants.py - Fusion processing → Reference data: loads reference
workflow/scripts/prioritization/fusions.py - Variant effects → Reference data: uses annotation and counts
workflow/scripts/prioritization/effects.py - Variant effects → Variant effects tables: writes
workflow/scripts/prioritization/effects.py - Prioritization entry → MHC binding prediction: starts prediction
workflow/scripts/prioritization/compile.py - MHC binding prediction → Neoepitope tables: writes
workflow/scripts/prioritization/prediction.py - Prioritization entry → Immunogenicity and similarity: scores epitopes
workflow/scripts/prioritization/compile.py - Workflow orchestration → Reporting: runs reporting
- Workflow orchestration → Summary: runs summary