Module: Bioinformatics Buffet
This module will cover the introductory materials of a broad range of topics in bioinformatics.
Monday: Introduction to Galaxy and Genomics
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.session page.
This session provides an introduction to Genome Assembly
An Introduction to Genome Assembly (Lecture)
Chloroplast genome assembly (Lecture & Tutorial)
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.
CRISPR screen analysis (Lecture)
CRISPR screen analysis (Tutorial)
To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene is often used. This allows us to identify the bacterial species present in our sample. This lecture and practical session introduces you to 16S analysis in Galaxy using the mothur tool suite.
Introduction to metagenomics (Lecture)
16S Microbial Analysis with mothur (short) (Tutorial)
In this 3-part module, you will learn about Nanopore long-read sequencing for the detection of antimicrobial resistance (AMR). There is a short video showing you the wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, and finally a practical tutorial walking you through an AMR analysis in Galaxy.