• Updates for existing chapters:

    • Rust Basics.
    • Alignment:
      • Create a simple multiple sequence aligner?
    • Kmers:
      • Syncmers (basics)

  • Suggestions for new chapters:

    • Blueprint:
      • Clap argument parsing.
      • Run commands from cli/subprocess.
      • Reading file to DataFrame.
      • Reading fast(a/q) with needletail.
      • Reading fast(a/q) with bio.
    • Amplicon:
      • In Silico PCR.
      • Cluster reads similar to isONclust3.
      • Classification.
    • Aminoacids:
      • Translation.
      • Alignment with substitution matrix?
    • Assembly:
      • The basics of assembly.
      • Build a De-Bruijn graph.
      • Build an overlap graph.
      • Eularian walk?
      • Section about the difficulties and challenges with assembly.
    • Pipelines (how do we solve dependencies in mdbook?):
      • Basic BLAST pipeline.
      • Basic read alignment pipeline.
      • Basic assembly pipeline.
      • Metagenomic classification with sylph.
      • SINTAX classifier in Rust.