This modules covers the basics of sequence analysis, including Quality Control (QC), mapping, and genome assembly.
Introduction to Genome analysis
These videos cover the most common steps in -omics analysis; Quality control, followed by either mapping or assembly, depending on the availability of a reference genome.
In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.
Quality Control (Lecture)
Quality Control (Tutorial)
In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.
This session provides an introduction to Genome Assembly
An Introduction to Genome Assembly (Lecture)
Chloroplast genome assembly (Lecture & Tutorial)
Advanced Genomics Analyses
After data cleaning, we can move on to the core of our analysis, depending on our analysis question. Below are some examples of such genome analyses.
Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.
M. tuberculosis Variant Analysis (Lecture)
M. tuberculosis Variant Analysis (Tutorial)
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. This session will introduce ATAC-Seq and walk you through an analysis step by step.
ATAC-Seq data analysis (Lecture)
ATAC-Seq data analysis (Tutorial)
This lecture will introduce the basic concepts involved in CRISPR screen analysis.