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Here are introductory materials to the world of k-mers in genomics. The series of tutorials is modual and allow the reader to jump in between them.

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Table of content

Introduction

• Concept of k-mers

k-mer spectra analysis

• 📖 Introduction to K-mer spectra analysis
  • ⚒ Generating k-mer spectra tutorial
• 📖 Basics of genome modeling
  • ⚒ manual model fitting (for better understanding of the underlying model)
  • ⚒ simple diploid
• 📖 Common difficulties in characterisation of diploid genomes using k mer spectra analysis
  • ⚒ low coverage (pitfall) - to be merged
  • ⚒ very homozygous diploid
  • ⚒ highly heterozygous diploid
  • ⚒ Genome size of a repetitive genome (pitfall)
  • ⚒ Wrong ploidy (pitfall)
• 📖 Characterization of polyploid genomes using k mer spectra analysis
  • ⚒ Autotetraploid
  • ⚒ Allotetraploid
  • ⚒ Estimating ploidy (smudgeplot)
• 📖 Genome modeling as a quality control
  • ⚒ Contamination (pitfall)
  • ⚒ k-mers in an assembly (Mercury/KAT)
• 📖 Analysing genome skimming data
  • ⚒ Phylogenetic placement of samples (Skmer) & estimating genomic distance (APPLES)
  • ⚒ Double phylogenetic placement of mixed samples (MISA)
  • ⚒ Genome size estimation of skimming data (RESPECT)
  • ⚒ Contamination in skimming data (CONSULT)
  • 🖥️ Installation of tools to work with skimming data

Separation of chromosomes

• 📖Separate sub-genomes of an allopolyploid
• 📖Separating chromosomes by comparison of sequencing libraries
  • ⚒ Extracting sex chromosome k-mers from a male and female sample
  • ⚒ Extract k-mers specific to germ-line restricted chromosomes
  • ⚒ Matching k-mers to a reference (bwa-mem)
  • ⚒ Matching k-mers to sequencing reads (cookiecutter)

Species assignment using short k-mers

• 📖Identifying haplotypes within targeted amplicon sequencing datasets
  • ⚒ Performing species assignment from targeted amplicon sequencing data

Others

• 🖥️ Installation of the kmer_tools conda evironment
• 📖 Other k-mer resources

ARCHIVE

The content of previous versions of these tutorials (namely, the tutorials used in the 2021 OH-KNOW workshop), are available in the archive