Quality impact results is the universal first step for all sequencing methods. This protocol is for sequencing results in FASTQ format. FastQC allows for visualization of quality scores. Sequence trimming allows for removal of residual primer sequences and increases overall quality scores. Trimmomatic does both. CutAdapt cuts adapters from sequences. Sickle creates a sliding window for quality and length trimming of FASTQ files.Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window.