Next Generation Sequencing Technologies and Applications to

Infectious Diseases JCVI/NIAID Training Workshop ILRI, Nairobi, Kenya

August 22 - 28, 2013

AGENDA

THURSDAY AUGUST 22 2013

8:30 - 8:30 Arrival and Registration

8:30 - 9:00 Welcome remarks and outline of the workshop objectives

Appolinaire Djikeng (Director, BecA-ILRI Hub, Nairobi, Kenya)

LECTURE SESSION 1: LINUX

9:00-9:30 Lecture: Basics of Bioinformatics

9:30-10:30 Lecture: Introduction to LINUX

10:30-11:00 TEA/COFFEE BREAK

11:00-12:30 Lab session: Command line LINUX

12:30-2:00 LUNCH BREAK

2:00-3:00 More about Linux: managing data with the OS built-in tools

3:00-3:30 TEA/COFFEE BREAK

3:30-5:00 Lab session: Command line LINUX - continued

FRIDAY AUGUST 22 2013

9:00-09:45 Lecture: Unix Shell Programming

Shell Scripting Basics

9:45-10:30 Tutorial: Applying Unix

10:30-11:00 TEA/ COFFEE BREAK

11:00-12:30 Lecture: Command Redirection and Pipelines

12:30 - 2:00 LUNCH BREAK

2:00-3:00 Lab session: Applying Unix

3:00-3:30 TEA/ COFFEE BREAK

3:30-5:00 Hands-on session continued

JCVI/NIAID Session Start

MONDAY AUGUST 26 2013

8:30 - 9:00 Welcome and Overview of the Workshop

Maria Giovanni (NIAID/NIH) Karen Nelson (JCVI)

9:00 - 9:30 Introduction to Genomics and applications to Infectious Diseases

David Wentworth (JCVI)

Overview of viral projects, technology, microbiome, phylogenetics, zoonotic infections (bacterial and viral).

9:30 - 10:15 Introduction to 'omics applications

Karen Nelson

Marcus Jones

Microbiomes, metagenomes, metatranscriptomes and metaproteomes

10:15 - 10:45 TEA/COFFEE BREAK

10:45 - 11:45 Overview of Next Generation Sequencing Technologies and

Sanger sequencing.

Timothy Stockwell

Vivien Dugan

11:45 - 12:30 Introduction to Bioinformatic software tools and cloud

Timothy Stockwell

Vivien Dugan