Add preprocessing steps to the JupyterBook documentation and Readme file

[leilaicruz]

• Add the necessary preprocessing steps that are needed to perform after getting the raw data from the sequencing company and before input them into the pipeline.
  • extracting the forwards reads (if we have paired end sequencing data)
  • right trim after the first restriction site sequence for NlaIII and DpnII , and discard the reads that after trimming are less than 100bp