This repository is a compilation of scripts created to automate and facilitate the processing of Fastq files. All scripts were created as a solution to specific problems but were kept as general as possible in order to enable others to use them in their own work.
Before running any script make sure to read the annotations in each and to verify that your directory structure matches the one assumed by the scripts (which should look like the following)
Feel free to use and adapt these scripts to your needs.