M. tuberculosis Bioinformatics Workshop
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  • Agenda and Lectures’ Slides
  • Day 1: Unix Shell Refresher for Bioinformatics
  • Day 2: Microbial Genome Assembly (from short and long reads) and Genome Annotation
  • Day 3: Read mapping and variant calling
  • Day 4: Phylogenetics/Phylogenomics and Building Reproducible Computational Pipelines
    • Datasets
    • Data Prep and Read QC
    • Processing and Merging SNVs from multiple isolates to get an MSA
    • Building Bioinformatics Pipelines with Snakemake
  • Day 5: Building Reproducible Computational Pipelines
M. tuberculosis Bioinformatics Workshop
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  • Day 4: Phylogenetics/Phylogenomics and Building Reproducible Computational Pipelines
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Day 4: Phylogenetics/Phylogenomics and Building Reproducible Computational Pipelines¶

  • Datasets
  • Data Prep and Read QC
  • Processing and Merging SNVs from multiple isolates to get an MSA
  • Building Bioinformatics Pipelines with Snakemake
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