GBprocesS

• Installation
  • Downloading the software
  • Installing GBprocesS in $HOME using pip
  • Installing GBprocesS in virtual environment using pip
  • Example installation
• Scope & Quick Start
  • Scope
  • Quick Start
  • Output
  • Debugging
• Operations
  • AverageQualityFilter
  • CutadaptDemultiplex
  • CutadaptTrimmer
  • LengthFilter
  • MaxNFilter
  • Pear
  • RemovePatternFilter
  • SlidingWindowQualityFilter
• Configuring INI-files: Examples
  • Restriction enzyme cutsite remnants and sequencing primers
  • Examples starting with Demultiplexing
  • Starting after Merging
• GBS data preprocessing: How it works
  • Read preprocessing steps
  • 0. Library preparation & Sequencing
  • 1. Demultiplexing
  • 2. Trimming
  • 3. Merging
  • Quality filtering
  • Read sequence filtering
  • Read length filtering
  • Why merge?
• Mapping and further processing
  • Single-digest GBS and single-end sequencing
  • Single-digest GBS and paired-end sequencing, mapped separately
  • Single-digest GBS and paired-end sequencing, merged
  • Double-digest GBS and single-end sequencing
  • Double-digest GBS and paired-end sequencing, mapped separately
  • Double-digest GBS and paired-end sequencing, merged