Run the first_script.sh line by line through whatever command line interface you prefer. Change all file plaths to the locations on your laptop.
FASTQ files from Nanopore basecalling should be converted into FASTA files before running the analaysis.
CAP3 analysis program should be run out of the downloaded CAP3 file, where CAP3 is the main file and cap3 is the executable located within that file. It can be found here https://faculty.sites.iastate.edu/xqhuang/cap3-assembly-program and download either the liinux 32 or 64 files. The paper associated with CAP3 is here https://pubmed.ncbi.nlm.nih.gov/10508846/ for ease of use and understanding of the program.