Week 1: Programming Fundamentals with Python

VSCode setup, Variables, data-structures, loops, conditionals

Scripting for automating repetitive tasks

Simulation: Mutation in DNA and why we need substitution models.

Exercise

Week 2: Introduction to BioPython

Functions: Introduction to Functional Programming.

Class: the big picture

Parsing FASTA and GenBank files. Sequence analysis and feature extraction.

Importance of commenting, docstrings and other good practices in programming

Assignment

Week 3: Essential Modules for Numeric Analysis

Jupyter Notebooks NumPy, Pandas, Matplotlib Plotting data with Seaborn

Understanding OOP, Converting scripts to CLI

Miniproject: Biochemical properties for TSS site prediction

Week 4: Introduction to R for data wrangling and visualization

Base R syntax, vector, data.frame

Fundamental data wrangling with filter, merge, pivot, group

Visualization with ggplot2

Week 5: Introduction to Unix

File system navigation, management, wildcards, permission, piping

awk, sed

Loop, conditional, Bash scripting

Week 6: Sequencing, Assembly, Annotation

Introduction to Sequencing, Genome Assembly, Genome Annotation, Public Data Utilization 

Week 7: Phylogenetic Analysis

Phylogenetic Methods Tree Visualization, Community Structure Analysis

Week 8: Ortholog Clustering and Pan-Genome Analysis 

Ortholog Detection, Pan-Genome Analysis, Microbial GWAS analysis, Phylogenomics

Week 9: Phylodynamics and Mobilome Analysis

Time-calibrated tree using beast, Identification and functional annotation of Plasmids and ICEs, Genomic Comparisons, Phylogenetic Networks

Week 10: Variant Calling

SNP Calling Pipelines Visualizing Variants Automating Analysis using Snakemake 

Week 11: Introduction to metagenomics

Taxonomic and functional profiling, shotgun metagenomics, MAGs, 

Week 12: Amplicon sequencing and metagenomics

Comparative metagenomics, diversity metrices,  Case-study 

Week 13-16: Project and support

Introduction to github
Independent project
Support