Bioinformatics Workshop - The Genomics Virtual Laboratory

& An Introduction to Microbial Genomics

Flinders University

Tuesday 22nd September 2015

URL: http://tinyurl.com/Bioinf-Flinders

Dieter Bulach, Simon Gladman, Harriet Dashnow

www.vlsci.org.au

Program

Time

Topic

Workshop materials

Other resources

9:00 - 9:15

Welcome, Introduction and Outline

Slides

9:15 - 9:45

The NeCTAR Cloud and the GVL

Slides

List of GVL instances

9:45 - 11:00

Intro to Galaxy

Slides

(Including morning tea)

Introduction to Galaxy Tutorial

The GVL website

www.genome.edu.au

Galaxy wiki

wiki.galaxyproject.org

11:00 - 12:30

NGS data

Slides

Microbial Genome Assembly

Slides

Genome assembly and annotation tutorial

SPAdes website

http://bioinf.spbau.ru/spades

GVL Assembly protocol

www.genome.edu.au/learn/learn#assembly

12:30 - 13:30

Lunch

13:30 - 14:15

Microbial Genome Annotation

Slides

Prokka website

https://github.com/tseemann/prokka

14:30 - 15:30

Microbial Variation

Slides

Read Mapping

Slides

Variant calling tutorial

Information on BWA

http://bio-bwa.sourceforge.net/

15:45 - 17:00

Variant Calling

Slides

Freebayes website

https://github.com/ekg/freebayes

Mauve website

http://darlinglab.org/mauve/mauve.html

17:00

Close

Workshop evaluation

embl-uom-vlsci-logo.jpeg