How gaolabtools/scnanogps works
scNanoGPS analyzes single-cell Nanopore reads through quality control, read scanning, barcode assignment, UMI-based consensus curation, and reporting of expression, isoforms, and mutations. The README documents these stages and the wrapper as the convenient entry point; the tree supports separate scripts for the major components. Some stage-to-stage connections below reflect that documented workflow rather than inspected orchestration code, and unsampled implementations are represented only by their existing paths.
Main entry points: run_scNanoGPS.py Pipeline wrapper · curator.py Read curator · scanner.py Read scanner · assigner.py Barcode assigner
Components 19
Pipeline stages
- Pipeline wrapper
run_scNanoGPS.py - Read QC
other_utils/prepare_read_qc.py - Read scanner
scanner.py - Pattern search
scanner_core/searching_core.py - Barcode assigner
assigner.py - Barcode merging
assigner_core/wrapping.py
Read processing
- Read curator
curator.py - Alignment and UMI
curator_core/curator_io.py
Cell reports
- Expression reporter
reporter_expression.py - Isoform reporter
reporter_isoform.py - SNV reporter
reporter_SNV.py - Summary reporter
reporter_summary.py
Analysis utilities
- Fusion finder
other_utils/find_fusion_isoform.py
Other components
- Researcher
- Nanopore reads
- Genome reference
- Minimap2
- SPOA
- Cell profiles
Connections 28
- Researcher → Pipeline wrapper: runs
- Researcher → Nanopore reads: provides
- Pipeline wrapper → Read QC: runs QC
- Pipeline wrapper → Read scanner: runs scan
- Pipeline wrapper → Barcode assigner: runs assignment
- Pipeline wrapper → Read curator: runs curation
- Pipeline wrapper → Expression reporter: runs reporting
- Pipeline wrapper → Isoform reporter: runs reporting
- Pipeline wrapper → SNV reporter: runs reporting
- Pipeline wrapper → Summary reporter: runs reporting
- Nanopore reads → Read QC: reads
- Nanopore reads → Read scanner: scans
- Read scanner → Pattern search: searches patterns
- Read scanner → Barcode assigner: barcode counts
- Barcode assigner → Barcode merging: merges barcodes
- Barcode assigner → Read curator: barcode list
- Read curator → Alignment and UMI: processes alignments
- Read curator → Minimap2: maps reads
- Minimap2 → Genome reference: uses
- Read curator → SPOA: collapses reads
- Read curator → Expression reporter: curated reads
- Read curator → Isoform reporter: curated reads
- Read curator → SNV reporter: curated reads
- Expression reporter → Cell profiles: expression matrix
- Isoform reporter → Cell profiles: isoform calls
- SNV reporter → Cell profiles: mutation profiles
- Summary reporter → Cell profiles: summary
- Fusion finder → Cell profiles: fusion analysis