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Overview

Welcome to this introductory course about NGS data analysis. During this course you will learn the basics of NGS data analysis and visualization in a Linux environment, current used software and best practices will be explained. This course is focused in NGS data alignment for DNA, variant calling, annotation, association and data visualization.

This is course is scheduled for 2 days and assumes a very basic knowledge of NGS data analysis and Linux. All materials in this is course are free and open, feel free to reuse them as you want. All the data for the tutorials are available in our DropBox folder.

Schedule

Day 1

During this first day we will start with an introduction to NGS technology and in the data preparation for their analysis. You will also learn the basics of the GNU/Linux shell introduction. At this point we are ready to start preparing and working with the data: Quality Control (QC) and NGS data alignment.

Course Presentation
Introduction to NGS technologies

Javier Santoyo, an overview about NGS technologies and some concepts.

Introduction GNU/Linux shell
Quality control for NGS raw data (FASTQ)
DNA and RNA-seq NGS read alignment
Visualization of mapped reads

Day 2

During the second day we will focus on Variant Calling, annotation and prioritization together with the visualization of VCF files.

Germline variant calling
Somatic variant calling and de novo mutations
Variant filtering and annotation
Variant association and prioritization
Big Data analysis and visualization

About

You can ask any question to Marta Bleda ([email protected]) and Ignacio Medina ([email protected]).

[www.ngscourse.com](http://www.ngscourse.org/)