Packages used (available through conda)

seqkit - a tool to view, parse and manipulate FASTA/FASTQ files, essential

seqtk - another tool to view, parse and manipulate FASTA/FASTQ files, optional

spades - a program for de novo assembly website, essential, already installed

velvet - an older program for de novo assembly website, optional

fastqc - a program to create a quality report of NGS files, already installed

jellyfish - tool to count k-mer occurrences in DNA sequences, optional, already installed