Welcome to kbbq’s documentation!

For a quick introduction, check out the Quickstart tutorial.

Contents:

• Tutorials
  • Quickstart
    • Installation
    • Recalibrate Reads
    • Benchmark Quality Scores
    • Plotting Benchmarked Scores
  • Installation
    • Virtual Environments
    • Creating a Virtual Environment with pipenv
    • Creating a Virtual Environment with conda
    • Creating a Virtual Environment with venv
    • Testing that installation was successful
  • Example Recalibration Workflow
    • Software Requirements
    • Downloading the Data
    • Recalibrating a BAM file
    • Correcting Reads
    • Calibrating FASTQ Reads
    • Benchmarking Calibration
    • Plotting the Benchmark
• Command Line Reference
  • Command Line Help
    • recalibrate
    • benchmark
    • plot
  • FASTQ Input Help
    • FASTQ Input Requirements
      • Inferring Read Groups
      • First or Second in Pair
      • Benchmark Read Matching
    • Converting from BAM to FASTQ
• Module Reference
  • kbbq
    • kbbq.recaltable
    • kbbq.compare_reads
    • kbbq.plot
    • kbbq.benchmark
    • kbbq.read
    • kbbq.covariate
    • kbbq.gatk
      • kbbq.gatk.bqsr
      • kbbq.gatk.applybqsr
    • kbbq.bloom
    • kbbq.recalibrate

Indices and tables

• Index
• Module Index
• Search Page