Page Index - KamilSJaron/k-mer-approaches-for-biodiversity-genomics GitHub Wiki

97 page(s) in this GitHub Wiki:

• Home
• Table of content
• ARCHIVE
• 2021_Advanced use of k mers for analyzing skimming data
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• 2021_Bash refresher
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• 2021_Characterization of genomes using k mer spectra analysis_SAGA
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• 2021_Flash talks
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• 2021_Introduction to K mer spectra analysis
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• 2021_Introduction to k mers for analyzing skimming data
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• 2021_Separate sub genomes of an allopolyploid
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• 2021_Separating chromosomes by comparison of sequencing libraries
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• Allotetraploid
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• Analysing genome skimming data
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• Autotetraploid
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• Basics of genome modeling
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• Characterization of diploid genomes using k mer spectra analysis
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• Characterization of polyploid genomes using k mer spectra analysis
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• Common difficulties in characterisation of diploid genomes using k mer spectra analysis
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• Concept of k mers
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• Contamination
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• Contamination in skimming data (CONSULT)
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• demonstrating the effect of sequencing error rate on k mer coverage
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• Double phylogenetic placement of mixed samples (MISA)
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• Estimating ploidy
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• Extract k‐mers specific to germ‐line restricted chromosomes
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• Extracting sex chromosome k‐mers from a male and female sample
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• Generating k mer spectra tutorial
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• Genome modeling as a quality control
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• Genome size estimation of skimming data (RESPECT)
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• Genome size of a repetitive genome
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• Highly heterozygous diploid
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• Identifying haplotypes within targeted amplicon sequencing datasets
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• Installation of the kmer_tools conda evironment
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• Installation of tools to work with skimming data
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• Introduction to K mer spectra analysis
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• k mers in an assembly
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• Low coverage
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• Manual model fitting
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• Matching k‐mers to a reference
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• Matching k‐mers to sequencing reads
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• other k mer resources
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• Phylogenetic placement of samples (Skmer) & estimating genomic distance (APPLES)
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• Running k mer tools in GitPod
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• Separate sub genomes of an allopolyploid
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• Separating chromosomes by comparison of sequencing libraries
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• Simple diploid
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• Species assignment using targeted amplicon sequencing datasets
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• Using short k mers to quantify similarity between samples from targeted amplicon sequencing data
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• Very homozygous diploid
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• Wrong ploidy
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