Microbial Genome Assembly and Annotation in Galaxy

Bioinformatics Training Room, Cambridge University.

June 8 2017

http://tinyurl.com/cambridge-assembly-2017

Simon Gladman, Gabriella Rustici, ...

Program

Time

Topic

Workshop materials

Other resources

9:30 - 9:45

Welcome, Introduction and Outline

Slides

NeCTAR Cloud

GVL Web Site

CLIMB Cloud

9:45 - 10:45

(Including a 10 minute break at 10am)

Galaxy 101

Slides

Galaxy 101 Tutorial

Galaxy website

http://galaxyproject.org

Galaxy Melbourne

10:45 - 12:30

NGS Data

Slides

Microbial Genome Assembly

Slides

Assembly with Velvet and Velvet Optimiser Tutorial

K-mer Value and Velvet Result Spreadsheet

Velvet paper

doi: 10.1101/gr.074492.10

Velvet website

12:30 - 13:30

Lunch

13:30 - 14:30 (including a 10 minute break at 14:30)

Microbial Genome Assembly (continued)

Assembly with SPAdes Tutorial

SPAdes website

http://bioinf.spbau.ru/spades

14:30 - 16:30

Microbial Genome Annotation

Slides

Microbial Genome Annotation with Prokka Tutorial

Prokka website

https://github.com/tseemann/prokka

16:30 - 16:45

Wrap up and close

http://galaxy-mel.genome.edu.au

Other Galaxy Servers:

https://usegalaxy.org

http://abrpi.genome.edu.au

Links to more training material:

https://sepsis-omics.github.io/tutorials

https://galaxyproject.github.io/training-material

https://gvl.org.au/learn

Thanks!