Fig. 1

Batch directory structure used by Cpipe. Each analysis is conducted using a standardised directory structure that separates raw data, design files and generated results from each other. All computed results of the analysis are confined to the ‘analysis’ directory, while source data is kept quarantined in the ‘data’ directory. The analysis directory keeps separate directories for each stage of the analysis starting with initial quality control (fastqc), alignment (align), variant calling (variants) and final quality control (qc). The final analysis results are placed in the ‘results’ directory