This repository contains scripts to analyze eDNA amplicon sequencing data as generated in a collaborative project between INBO (Research Institute for nature and Forest) and ILVO (Flanders Research Institute for Agriculture, Fishieries and Food) (Belgium). It contains a demultiplexing shell script, capable of demultiplexing dual-indexed libraries with in-line barcodes of variable size on undirectionally ligated fragments. It also contains a shell script to fully automate the subsequent analyses including primer removal, merging of forward and reverse reads, quality filtering and count table generation (depending on third party software). A README.md markdown document is included with more information.