Brioche documentation

Landing page

Main

• Introduction
  • Brioche overview:
  • Key features:
  • Key use cases:
  • Workflow summary:
  • User guide:
• Installation
  • Downloading brioche:
  • Software dependencies:
  • File layout:
• Setting up a run
  • Brioche inputs:
  • Parameters file:
  • Run parameters and goals
  • Simple runs
• Results
  • Results folder structure
  • Summary report
  • Results files
  • Other results files
  • Brioche usecases
• Citations
• FAQ
  • 1. How many markers can brioche analyse in a single analysis?
  • 2. What are the best settings to run Brioche on?
  • 3. The DArT scripts don’t seem to work?
  • 4. Some analysis steps seem to be taking a very long time or are restarting why is that?
  • 5. Brioche seems to crash and not install the conda environments
  • 6. I don’t have access to many modules and can’t load Nextflow/R etc
  • 7. My HPC does not use slurm it uses PBS/QSUB/LSF/SGE etc.
  • 8. Brioche crashed and nothing above helps

Use cases

• Usecase1: Remapping data across reference genomes
  • Requirements
  • Runfile
  • Outputs
• Usecase2: In silico genotyping of reference genomes
  • Requirements
  • Runfile
  • Outputs
• Usecase3: Testing redundancy/accuracy in marker datasets
  • Requirements
  • Runfile
  • Output
  • Extensions
• Usecase4: Merge datasets
  • Requirements
  • Runfile
  • Outputs