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