Course Overview
The development of next generation sequence technology has led to rapid advances in microbiome study. The Sydney Brenner Institute for Molecular Bioscience with support from the Pan-African Bioinformatics Network for H3Africa will be offering a short-course on the bioinformatics of analysing the microbiome. The course will give an overview of conducting a microbiome study, present some of the most important techniques, and will include some hands-on use of some the key tools. The course will cover analysis both using both 16S RNA gene sequences and shotgun sequencing

Intended Audience
The workshop is aimed at individuals of research groups within the University of the Witwatersrand and associated Institutions, AWI-Gen and H3Africa members that will be working on analysing microbiome data

Keywords: 16S, Microbiome, NGS, Genomics, Nucleic acid analysis

Skill level of training: Intermediate

Language: English

Credential awarded: No credential awarded

Type of training: Face-to-face

Venue of the course: University of the Witwatersrand, Johannesburg, South Africa

Dates for the course: Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT

Course organisers: Professor Scott Hazelhurst, Professor Nicola Mulder, Ami Bhatt, Gerrit Botha, Africa Wits-INDEPTH Partnership for Genomic Research, Sydney Brenner Institute for Molecular Bioscience, H3ABioNet

Participation: There is a small fee associated with the participation of this workshop to help cover costs. This includes the cost of the workshop, but does not include lunches or tea breaks. The fees are: R500: Members of Wits and associated institutions (this is defined as being the ability to pay with a Wits internal requisition; if you can't pay with an I/R you need to pay the external rate). R600: Other research and non-profit institutions. R1200: For profit company. H3ABioNet travel fellowship awardee: No course fee will be levied (please see below for more information on applying for an H3ABioNet travel fellowships) N.B – Due to the limited number of places, workshop participation selection will be done on a competitive basis through the completed application form.

Course Sponsors: Africa Wits-INDEPTH Partnership for Genomic Research, Sydney Brenner Institute for Molecular Bioscience, H3ABioNet

Course objectives

• Participants will gain an overview of conducting a microbiome study
• Sample collection and DNA extraction
• Taxonomic approaches and diversity
• Analysing 16S rRNA data
• Assembly of metagenomic data
• Gene prediction and functional annotation
• Key microbiome databases and tools

Prerequisites

A working knowledge of the Linux command line. An introductory workshop on Linux will be provided on the 27th of March. To apply to attend this, please visit: http://www.bioinf.wits.ac.za/courses/linux17

Participants are also encouraged to go over some of the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://ryanstutorials.net/linuxtutorial/commandline.php 
http://www.h3abionet.org/tools-and-resources/sops/16s-rrna-diversity-analysis
http://qiime.org/tutorials/ 
https://www.youtube.com/watch?v=pOV_tuZqzso&t=187s
https://joey711.github.io/phyloseq/import-data.html 
http://research.computing.yale.edu/support/hpc/user-guide/submitting-jobs-using-torque

Course limitations
This workshop will provide a foundation for continued learning in the bioinformatics handling of microbiome data, approaches to microbiome taxonomic and diversity analyses identification and associated tools and databases. This workshop will not make one an expert on the study design and analyses of microbiome data as it is an introductory workshop.

Training material availability

Training materials for this course are available as a single downloadable archive here: https://doi.org/10.25375/uct.19129943. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.