Bioinformatics Workshop - The Genomics Virtual Laboratory

& An Introduction to Microbial Genomics

UWA and Harry Perkins - Perth 2016

Tuesday 22nd & Wednesday 23rd November

URL: tinyurl.com/microbial-perth-2016

Anna Syme, Simon Gladman, Su Chen Lim, Rachael Lappan, Sarah Beecroft

www.vlsci.org.au, www.uwa.edu.au

Program Tuesday 22nd November

Time

Topic

Workshop materials

Other resources

9:00 - 10:30

Welcome, Introduction and Outline (Simon)

Slides

The NeCTAR Cloud and the GVL (Simon)

Slides

List of GVL instances

The GVL website

www.genome.edu.au

Intro to Galaxy (Anna)

Slides

Introduction to Galaxy Tutorial

Galaxy wiki

wiki.galaxyproject.org

10:30 - 11:00

Morning tea

11:00 - 12:30

NGS data (Simon)

Slides

Microbial Genome Assembly (Simon)

Slides

Assembly with Velvet and Velvet Optimiser Tutorial 

K-mer Value and Velvet Result Spreadsheet

Link to galaxy history data:

https://swift.rc.nectar.org.au:8888/v1/AUTH_377/public/Microbial_tutorials/Galaxy_history_input_files.tar.gz

How to upload this data:

http://sepsis-omics.github.io/tutorials/modules/data-dna/

Velvet paper

doi: 10.1101/gr.074492.10

Velvet website

12:30 - 13:30

Lunch

13:30 - 15:00

Microbial Genome Assembly Continued

Assembly with Spades Tutorial

SPAdes website

http://bioinf.spbau.ru/spades

15:00 - 15:30

Afternoon break

15:30 - 17:00

Microbial Genome Annotation (Anna/Simon)

Slides

Annotation Tutorial

Prokka website

https://github.com/tseemann/prokka

17:00

End of Day 1

Program Wednesday 23rd November (Times are yet to be confirmed)

Time

Topic

Workshop materials

Other resources

9:00 - 9:15

Welcome: Day 2 (Anna)

Slides

9:15 - 10:30

Read mapping (Simon)

Slides

Variant Calling (Simon)

Slides

Read Mapping Tutorial

Variant Calling Tutorial

Snippy link

Information on BWA

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

Freebayes website

https://github.com/ekg/freebayes

10:30 - 11:00

Morning tea

11:00 - 12:30

Comparative genomics with Mauve (Simon)

Slides

Comparative genomics tutorial

Demonstration (no tutorial)

Mauve website

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

12:30 - 13:30

Lunch

13:30 -15:00

RNA-Seq and Microbial Transcriptomics (Anna)

Slides

RNA-seq Tutorial

15:00 - 15:30

Afternoon break

Workshop evaluation

15:30 - 16:30

RNA-Seq and Microbial Transcriptomics continued

Questions and Discussion (Simon)

Summary slides

Long read tutorial

http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly/

16:30

Close

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