Agenda and Lectures’ Slides¶
Wednesday¶
AM¶
- Lecture:
Whole-genome sequencing: technologies and data
- Overview of short and long read sequencing technologies
- Project design considerations: library complexity, data quantity and quality
- Lecture:
Genomics of M. tuberculosis and Genome Assembly Algorithms
- Short intro to genomics and population genomics of M. tuberculosis
- Reference-based, de-novo, and hybrid genome assembly
PM¶
- Hands-on computer lab:
- Short and Long Read Genome Assembly
- Assembly Quality Control
- Genome Annotation
Thursday¶
AM¶
Lecture: Read Mapping and variant calling
PM¶
- Hands-on computer lab:
- Read mapping
- Variant calling
Friday¶
AM¶
Lecture: Microbial phylogenetics and phylogenomics
Lecture: Reproducible research in high-throughput biology and building bioinformatics pipelines
PM¶
- Hands-on practical:
- M. tuberculosis phylogenetics and phylogenomics
- Building computational pipelines with Snakemake