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This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.

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RADSeq-Pipeline

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;

  1. Demultiplexing
  2. Data cleaning
  3. Read alignment
  4. Alignment sorting
  5. Loci catalog
  6. QC
  7. Analysis
  8. Annotation

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This repository contains a number of bash and R scripts used in the processing of RADSeq data on the VSC supercomputer.

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