breseq Manual

Contents:

• Introduction
• Installation
  • 1. Install external dependencies
    • MacOSX Instructions
  • 2. Compile and install breseq
    • Installing in a system-wide location
    • Installing in the source directory
    • Installing in a custom location
  • Common installation problems
    • Dependencies installed in custom locations
    • Other problems
• Usage
  • breseq
  • breseq bam2aln
• 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
    • Haploid Bayesian SNP caller
    • Polymorphism Prediction
  • 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
• Output
  • HTML Archive
    • Mutation Display
    • Evidence Display
  • Processed Data
  • Viewing Output / Aligned Reads in the IGV
• References
• Acknowledgments
  • Developers
  • Testers
  • Funding

Appendices:

• GenomeDiff Utility
• GenomeDiff Format

Documentation last updated September 10, 2011.