Agenda and Lectures’ Slides

Tuesday

PM

Intermediate to Advanced Unix Shell for Bioinformatics

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

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

Saturday

AM

Lecture & Practical: Building computational pipelines with python and Snakemake