Training material for the course "Exome analysis with GALAXY"

Galaxy is an open source, web-based platform for data intensive biomedical research. It makes accessible bioinformatics applications to users lacking programming skills, enabling them to easily build analysis workflows for NGS data.<br>
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The course "<strong>Exome analysis using Galaxy</strong>" is aimed at PhD student, biologists, clinicians and researchers who are analysing, or need to analyse in the near future, high throughput exome sequencing data. The aim of the course is to make participants familiarise with the Galaxy platform and prepare them to work independently, using state-of-the art tools for the analysis of exome sequencing data.

The course will be delivered using a mixture of lectures and computer based hands-on practical sessions. Lectures will provide an up-to-date overview of the strategies for the analysis of exome next-generation experiments, starting from the raw sequence data. Analyses include sequence quality control, alignment to a reference genome, refinement of aligned sequences, variant calling, annotation and interpretation, and tools for visual inspection of results. Participants will apply the knowledge gained during the course to the analysis of Illumina’s real exome datasets, and implement workflows to reproduce the complete analysis. After the course, participants will be able to create pipeline for their individual analyses.

Those are the needed datasets for this course.

Galaxy是一款开源的、基于网页的面向数据密集型生物医学研究的平台。它为不具备编程技能的用户提供了生物信息学应用的访问途径，使其能够轻松构建针对下一代测序（Next-Generation Sequencing）数据的分析工作流。

本课程<strong>使用Galaxy进行外显子组分析</strong>面向正在或即将开展高通量外显子组测序数据分析的博士生、生物学家、临床医师及研究人员。课程目标是让学员熟悉Galaxy平台，并使其能够独立运用前沿工具开展外显子组测序数据分析工作。

本课程将结合讲座与基于计算机的实操实训环节开展授课。讲座将系统梳理外显子组下一代测序实验的分析策略，从原始序列数据起步，涵盖序列质量控制、参考基因组比对、比对序列优化、变异检出、注释与解读，以及用于结果可视化检视的各类工具。学员将运用课程所学知识，对Illumina公司的真实外显子组数据集开展分析，并构建工作流以复现完整的分析流程。课程结束后，学员可独立搭建适用于自身研究的分析流水线。

以下为本课程所需的数据集。