How yukiteruono/pbsim3 works
PBSIM is a command-line long-read sequencing simulator. The documented workflow selects a sequencing strategy and simulation method, reads reference or user-provided sequence data and applicable model/profile data, simulates reads and errors, then emits reads and alignments. The implementation is concentrated in src/pbsim.cpp; the README documents several modes beyond the sampled code excerpts, so their internal wiring is represented only where supported. Multi-pass output can be passed to external CCS software to generate HiFi reads.
Main entry points: pbsim.cpp CLI and dispatch · QSHMM-RSII.model QSHMM models · ERRHMM-RSII.model ERRHMM models
Components 18
Run orchestration
- CLI and dispatch
src/pbsim.cpp
Simulation modes
- WGS simulation
src/pbsim.cpp - Transcript simulation
src/pbsim.cpp - Template simulation
src/pbsim.cpp
Models and sampling
- Quality model
src/pbsim.cpp - Error model
src/pbsim.cpp - Read sampling
src/pbsim.cpp - QSHMM models
data/QSHMM-RSII.model - ERRHMM models
data/ERRHMM-RSII.model - Sample profiles
Output and integration
- Read and alignment files
Other components
- PBSIM user
- Reference genome
- Transcript inputs
- Template inputs
- Real read data
- gzip
- CCS software
Connections 23
- PBSIM user → CLI and dispatch: configures
- CLI and dispatch → WGS simulation: dispatches
- CLI and dispatch → Transcript simulation: dispatches
- CLI and dispatch → Template simulation: dispatches
- WGS simulation → Reference genome: reads
- Transcript simulation → Transcript inputs: reads
- Template simulation → Template inputs: reads
- WGS simulation → Quality model: uses
- WGS simulation → Error model: uses
- WGS simulation → Read sampling: uses
- Transcript simulation → Quality model: uses
- Transcript simulation → Error model: uses
- Template simulation → Quality model: uses
- Template simulation → Error model: uses
- Quality model → QSHMM models: loads
- Error model → ERRHMM models: loads
- Read sampling → Real read data: reads
- Read sampling → Sample profiles: stores or reuses
- WGS simulation → Read and alignment files: writes
- Transcript simulation → Read and alignment files: writes
- Template simulation → Read and alignment files: writes
- CLI and dispatch → gzip: compresses MAF
- CLI and dispatch → CCS software: provides multi-pass BAM