Introduction to Next Generation Sequencing Bioinformatics

A Tufts University Research Technology Workshop

Description

This course covers the basics of Next Generation Sequencing Bioinformatics, with the goal of variant calling and interpretation.

The material is designed to be a 3 hour workshop and is run on Tufts High Performance Compute (HPC) Cluster. For support with this workshop or the HPC cluster, email TTS Research Technology tts-research@tufts.edu

If you are taking this workshop on 5/19/20, please use Piazza for discussion. The class is listed in term Summer 2020, 1: Intro to NGS Bioinformatics

Goals

• Writing and running bash scripts on the HPC
• Intro to several bioinformatics tools: BWA, Samtools, Picard, GATK, VEP, IGV
• Variant Calling, Annotation and Interpretation using a Human Exome sample

Prerequisites

Computational skills needed

• Introduction to Linux
• Introduction to HPC

Materials Needed

• Chrome web browser
• Account on Tufts HPC
• VPN if accessing the HPC from off campus

Schedule

• Introduction
• Setup
• Quality Control
• Alignment
• Alignment Cleanup
• Variant Calling
• Annotation and Interpretation

Acknowledgement

Much of this workshop has been adapted from the HBC Training In Depth NGS Analysis Course with the help of Dr. Wenwen Huo at Tufts University.