breseq Manual

Contents:

• Introduction
  • Citing breseq
• Installation
  • Install external dependencies
  • Method 1. Binary download
  • Method 2. Source code download
    • Installing in a system-wide location
    • Installing in the source directory
    • Installing in a custom location
  • Method 3. GitHub source code
  • Installing on Windows (using WSL)
  • Installing on Galaxy
  • Troubleshooting installation
• Usage Summary
  • breseq
  • Command: bam2aln
  • Command: bam2cov
• Test Drive
  • 1. Download data files
    • Reference sequence
    • Read files
  • 2. Run breseq
  • 3. Open breseq output
• Methods
  • Read mapping
  • New junction evidence (JC)
    • Identifying candidate junctions
    • Scoring and accepting junctions
  • Read alignment evidence (RA)
    • Read end trimming
    • Base quality re-calibration
    • Calling mutations from RA evidence
    • Consensus score (Bayesian SNP caller)
    • Polymorphism score (mixed allele model)
    • Statistical filters for RA predictions
    • RA prediction options and flowcharts
  • Unknown base evidence (UN)
  • Missing coverage evidence (MC)
    • Read coverage distribution
    • Seed and extend algorithm
  • Mutation prediction
    • Base substitutions
    • Short insertions and deletions
    • Large deletions
    • Mobile element insertions
    • Duplications
    • Other evidence
  • Limitations
  • Annotated bibliography
• Output
  • HTML (Human-Readable) Output
    • Mutation Display
    • Evidence Display
  • Processed (Computer-Readable) Data
  • Viewing Output / Aligned Reads in the IGV
• References
• Acknowledgments
  • Developers
  • Testing
  • Funding

Tutorials:

• Tutorial 1: Clonal Samples
• Tutorial 2: Mixed Populations
• Tutorial 3: Consensus Reads and Targeted Sequencing

Appendices:

• Frequently Asked Questions (FAQ)
• gdtools Utility
• Genome Diff Format
• Reference Sequence Format

Documentation last updated August 19, 2021.