Learn Galaxy

There are many approaches to learning how to use Galaxy. The most popular is probably to just dive in and use it. Galaxy is simple enough to use that you can do many analyses just by exploring the interface. However, you may miss much of the power this way.

Tutorials using Galaxy Main

These tutorials are using Galaxy's main site at http://usegalaxy.org:

  • Galaxy 101 - the basic introduction to Galaxy's interface, its functionality, and workflows. Start here if you never used Galaxy before.
  • Uploading data - how to get data into Galaxy.
  • Histories - in Galaxy uploaded data and analysis results reside within the history pane. This tutorial explains how history works.
  • Dataset collections - modern studies usually include many samples. Collection are designed to simplify complex, multi-sample analyses as shown in this tutorial.
  • NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data.
  • Variant discovery: diploid case - this tutorial explains calling sequence variants in diploid systems like ... humans.
  • Variant discovery: haploid case - this tutorial explains calling sequence variants in haploid systems like ... bacteria and viruses.
  • RNA-seq: Introduction - an introductory tutorial for transcriptome analysis.
  • RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example.
  • ChIP-seq: A simple ChIP-seq experiment with two replicates - an example analysis for finding transcription factor binding sites.

Interactive Tours

Tours guide you through interface elements interactively:

Tutorials by Galaxy Training Network

Thanks to a large group of wonderful contributors there is a constantly growing set of tutorials maintained by the Galaxy Training Network. These include:

Tutorials from Lewis-Sigler Institute @ Princeton

These tutorials are produced by Lance Parsons at LSI

Tutorials from around the Web

In addition the following tutorials are available from other contributors:

Topic Authors Posted / Presented
Web-based Analysis of Next Generation Sequence Data Neerja Katiyar, Tyler Backman, Rebecca Sun, and Thomas Girke, UC Riverside 2013/12
Intro to Using Galaxy for Bioinformatics
Includes a transcriptome assembly example.
Ganote, Carrie L.; Doak, Thomas 2013//09
UC Davis 2013 Bioinformatics Short Course
Includes slides and exercises on almost everything.
Joe Fass, Nikhil Joshi, Jessie Li, Monica Britton, Blythe Durbin-Johnson 2013/09
Informatics on High Throughput Sequencing Data
Module 5 - Bringing it all together: Galaxy
Francis Oullette 2013/06
NGS in Galaxy
Includes ChIP-Seq, RNA-Seq and Exome-Seq examples.
Shannan Ho Sui, Oliver Hofmann, Winston Hide, Center for Health Bioinformatics at the Harvard School of Public Health 2013/05
Introduction to Galaxy 2013 Bootcamp Nikhil Joshi, Bioinformatics Core, UC Davis Genome Center 2013/02
RNA-seq Analysis in Galaxy BaRC, Whitehead Institute 2013/01
Performing de novo assemblies using the NBIC Galaxy instance Jan van Haarst (WUR) 2013/01
IIHG Bioinformatics Short Course
Downloadable PDFs cover Galaxy Intro and File formats, NGS Intro, Galaxy Basics, and Reproducibility and Collaboration within Galaxy
Ann Black-Ziegelbein, Tom Bair, Srinivas Maddhi 2013/01
NGS Analysis with Galaxy and IGV Tyler Backman, Rebecca Sun and Thomas Girke, UC Riverside 2012-12-10
Galaxy Tutorials
Including RNA-Seq, Variant Detection, and Genome Assembly
The Genomics Virtual Lab 2012/09-12
Analysis of ChIP-seq data in Galaxy BaRC, Whitehead Institute 2012/11
Next Generation Sequencing Data Analysis (Course no 11)
"Massively parallel sequencing, also known as next generation sequencing, is a technology enabling high-throughput sequencing of genomes or loci of interest. This course focuses on a single locus. It examines the quality of the sequence reads; mapping of reads; and the quality of the mapping. It also examines sequence variation." (slides)
Lynn Young 2012/09
Automated and reproducible analysis of NGS data (ARANGS12)
Day 4
Rutger Vos, Darin London 2012/09
Galaxy, a web based platform for bioinformatics analysis Bioinformatics & Research Computing @ MIT, as part of their Hot Topics series 2012/06
Using Galaxy for NGS Analysis Luce Skrabanek 2012/06
RNA-Seq Course v1.0 documentation UC Davis Bioinformatics Professional Training Program 2012/05
Analyzing epigenome data in context of genome evolution and human diseases Feuerbach, et al. 2012/02
UAB Galaxy RNA Seq Step by Step Tutorial Curtis Hendrickson 2011-09-16