this is a series of scripts (bash, R, python) and terminal commands intended to process and analyse RADSeq data. they are intended specifically for use the the Flemish Supercomputer Centre (VSC) high-performance compute cluster (HPC) and will likely not work elsewhere without appropriate modification.
Approximate order of operations;
- Demultiplexing
- Data cleaning
- Read alignment
- Alignment sorting
- Loci catalog
- QC
- Analysis
- Annotation