How avans-atls/fluqc works
FluQC turns influenza FASTQ samples and a reference database into per-sample QC data, then loads that data into an interactive dashboard. Preprocessing assigns reads and computes summary, mapping, coverage, read-length/quality, and putative-DIP metrics; the dashboard presents these as four documented pages. The sampled CLI and modules show the main orchestration and visualization calls. Some wrapper details are partial, so only visible tool invocations and documented workflow links are shown.
Main entry points: cli.py CLI Workflow · wrappers.py Analysis Wrappers · layout.py Dashboard Pages · samplepaths.py Sample Paths
Components 20
Preprocessing
- CLI Workflow
fluqc/cli.py - Sample Paths
fluqc/samplepaths.py - Analysis Wrappers
fluqc/wrappers.py - Read Assignment
fluqc/wrappers.py
QC Metrics
- QC Data
fluqc/figuredata.py - Summary Metrics
fluqc/figuredata.py - Mapping Metrics
fluqc/figuredata.py - DIP Estimates
fluqc/figuredata.py - Sample Metrics
fluqc/figuredata.py - Dashboard Data
fluqc/cli.py
Dashboard
- Plot Generation
fluqc/plotter.py - Dashboard Pages
fluqc/dashboard/layout.py - Page Explanations
fluqc/dashboard/texts.py
External Tools
- Minimap2
- Samtools
- Seqtk
Other components
- Operator
- FASTQ Samples
- Reference Database
- Local Browser
Connections 21
- Operator → CLI Workflow: runs
README.md - FASTQ Samples → CLI Workflow: analyzed by
README.md - Reference Database → CLI Workflow: supplied to
README.md - CLI Workflow → Sample Paths: creates paths
fluqc/cli.py - CLI Workflow → Analysis Wrappers: runs analysis
fluqc/cli.py - Analysis Wrappers → Minimap2: maps reads
fluqc/wrappers.py - Analysis Wrappers → Samtools: runs coverage
fluqc/wrappers.py - Sample Paths → Seqtk: subsamples with
fluqc/samplepaths.py - Analysis Wrappers → Read Assignment: assigns reads
fluqc/wrappers.py - CLI Workflow → QC Data: collects results
fluqc/cli.py - CLI Workflow → DIP Estimates: appends DIP metrics
fluqc/cli.py - CLI Workflow → Mapping Metrics: appends coverage metrics
fluqc/cli.py - CLI Workflow → Sample Metrics: appends sample metrics
fluqc/cli.py - CLI Workflow → Summary Metrics: appends summary
fluqc/cli.py - CLI Workflow → Dashboard Data: serializes
fluqc/cli.py - Dashboard Data → CLI Workflow: loaded by
fluqc/cli.py - CLI Workflow → Dashboard Pages: launches dashboard
fluqc/cli.py - Dashboard Pages → Plot Generation: creates plots
fluqc/dashboard/layout.py - Plot Generation → QC Data: reads metrics
fluqc/plotter.py - Dashboard Pages → Page Explanations: uses explanations
fluqc/dashboard/layout.py - Dashboard Pages → Local Browser: serves dashboard
README.md