For assistance with FastQC reports - https://biof-edu.colorado.edu/videos/dowell-short-read-class/day-4/fastqc-manual
Cutadapt is used for the removal of adapters near the 3' end of a read. The basic command-line for cutadapt is: cutadapt -a AAGTCAT -o output.fastq input.fastq
This will result in the removal of the adapter sequence AAGTCAT. All reads in the input file will also be present in the output file, however, some will be trimmed while others not.
Input file formats: FASTA (.fasta, .fa or .fna) and FASTQ (.fastq and .fq) Even when in a compressed file, cutadapt can read it
For assistance with cutadapt - https://media.readthedocs.org/pdf/cutadapt/stable/cutadapt.pdf
Once cut, reads will have to be filtered