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KamilSJaron edited this page Feb 7, 2023
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Introduction
k-mer spectra analysis
Separation of chromosomes
- Separate sub-genomes of an allopolyploid
- Separating chromosomes by comparison of sequencing libraries
Analysis of skimming data
Introduction
k-mer spectra analysis
- 📖 Introduction to K-mer spectra analysis
- 📖 Basics of genome modeling
- ⚒ manual model fitting (for better understanding of the underlying model)
- ⚒ simple diploid
- ⚒ demonstrating the effect of sequencing error rate on k-mer coverage
- 📖 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
Species assignment using short k-mers
Others