Introduction to NGS & GWAS

Brief introduction

We will introduce the students to Next-Generation Sequencing Technologies & GWAS and the software tools and approaches that are used to work with the data that is generated from NGS instruments.

 Topics Covered

•General overview of NGS Sequencing
•The Illumina Sequencing Platform
•Library Preparation
•Sequence Data Formats
•Sequence Quality Control and Pre-processing
•SAM/BAM formats
•Samtools, BedTools, PicardTools : Post-Processing
•Data Visualization
•Introduction to R
•Variant Calling
•VCF format
•Somatic Callers
•Variant Annotation
•RNA Seq
•Copy Number Variation
•Structural Variation
•Introduction to GWAS
•Plink Data Format
•Quality Control in GWAS
•Association Analyses
•GWAS in Africa


Expected Outcomes

Analysis of NGS data requires skills with a large number of computational tools and software packages as well as an understanding of the biology behind the analyses.  We will introduce the necessary skills and work through the use of a specific set of tools each addressing different needs that contribute to a full analysis pipeline.  Students should expect to leave with a better understanding of the skills and tools required as well as practical experience using the software and reviewing the results.  This will be a starting point upon which students can further develop these skills working with their own data.


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