Pipeline to process amplicon sequencing results.
Clone the pipeline by issuing:
git clone https://github.com/HeyLifeHD/amplicon_seq_pipeline/Change the directories of your working directory and reference genome in the config file. Put your fastq.gz files from an amplicon sequencing experiment into a a folder called "01_fastq_raw/" inside your specified working directory. In addition specify the location of the config file in the Snakefile. Now you are ready to go!