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Kamil S. Jaron edited this page Apr 4, 2024 · 33 revisions

Welcome to the oh-know wiki!

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.

If anything breaks, or you the input files are no where to be found. Please, opens us a an issue.

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

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 ttorials used in the 2021 OH-KNOW workshop), are available in the archive