How barricklab/breseq works
breseq analyzes sequencing reads against a reference genome to identify and report candidate mutations. The principal workflow is read/reference input, alignment and alignment resolution, evidence-based mutation identification, and GenomeDiff/output generation. Coverage analysis is a related branch that computes coverage summaries and plots. The tree and README establish the product’s identity, while the excerpts provide only partial implementation evidence; the graph therefore omits uncertain wiring and does not attempt to represent unsampled orchestration.
Main entry points: reference_sequence.cpp Reference handling · identify_mutations.cpp Mutation evidence · genome_diff.cpp GenomeDiff data · resolve_alignments.cpp Resolve alignments
Components 18
Inputs and configuration
- Read files
- Reference sequence
- Run settings
src/breseq/settings.cpp - FASTQ handling
src/breseq/fastq.cpp - Reference handling
src/breseq/reference_sequence.cpp
Read mapping
- Alignment operations
src/breseq/alignment.cpp - Samtools commands
src/breseq/samtools_commands.cpp - Resolve alignments
src/breseq/resolve_alignments.cpp
Evidence and analysis
- Read pileup
src/breseq/pileup.cpp - Mutation evidence
src/breseq/identify_mutations.cpp - Junction evidence
src/breseq/candidate_junctions.cpp - Coverage analysis
src/breseq/coverage_distribution.cpp - Mutation prediction
src/breseq/mutation_predictor.cpp - Reference annotation
src/breseq/reference_sequence.cpp
Results and reporting
- Coverage tables and plots
src/breseq/coverage_output.cpp - GenomeDiff data
src/breseq/genome_diff.cpp - Result reporting
src/breseq/output.cpp - Run summaries
src/breseq/summary.cpp
Connections 18
- Read files → FASTQ handling: provides reads
- Reference sequence → Reference handling: provides reference
- FASTQ handling → Alignment operations: read sequences
- Reference handling → Alignment operations: reference sequences
- Run settings → Resolve alignments: configures
- Samtools commands → Resolve alignments: alignment commands
- Alignment operations → Resolve alignments: alignment data
- Resolve alignments → Mutation evidence: resolved alignments
- Mutation evidence → Read pileup: pileup evidence
- Mutation evidence → Junction evidence: junction analysis
- Reference handling → Coverage analysis: reference sequences
- Coverage analysis → Coverage tables and plots: coverage statistics
- Mutation evidence → GenomeDiff data: records evidence
- GenomeDiff data → Mutation prediction: mutation entries
- Mutation prediction → GenomeDiff data: updates entries
- Reference handling → Reference annotation: annotates mutations
- GenomeDiff data → Result reporting: reported entries
- Run summaries → Coverage analysis: coverage statistics