Preprocessor

Initial data processing for PacBio amplicon data.

The preprocessor module performs the following operations:

• Combine raw data from multiple SMRT cells
• Transparently handle data from both RS2 and Sequel platforms
• Barcoding
• Demultiplexing
• CCS

Requirements

• Conda/Miniconda

Installation

• Clone the repository

  • git clone https://github.com/lumc-pgx/preprocessor.git

• Change to the preprocessor directory

  • cd preprocessor

• Create a conda environment for running the pipeline

  • conda env create -n preprocessor -f environment.yaml

Configuration

Pipeline configuration settings can be altered by editing config.yaml.

Execution

• Activate the conda environment
  • source activate preprocessor
• Run the pipeline using Snakemake