Course Overview
Last year's course was presented online due to COVID19, and due in part to positive responses received by participants, this year's course seeks to expand on that model. You should have received zoom contact information in your email which will be used for each day of the course.
The course is designed to have 2 ~90 minute sections per day for 5 days, with the goal of teaching you how to preform the standard next-generation sequencing analysis to identify genomic variants. This will be accomplished through: presentations covering information essential to all types of analysis, guided tutorials to reinforce the essential concepts, and optional self guided tutorials to help you learn the skills that are most specific to your own analysis. By the end of this course, we hope to achieve the following goals:
- Teach you different ways next generation sequencing libraries are constructed, and the advantages/disadvantages associated with the different types.
- Familiarize you with how the Texas Advanced Computing Center (TACC) can be used to simplify and speed up your data analysis.
- Introduce you to common ways of installing programs useful for NGS analysis.
- Teach you the basics of read mapping in both individuals and populations, and identifying variants within individuals and rare variants within populations.
- Provide reference materials covering a breadth of material sufficient to give you a starting point of where to begin you own data analysis, and enough experience that you can begin that analysis on your own.
Your Instructor
Name | Initials | Affiliation | Expertise |
|---|---|---|---|
Daniel Deatherage | DD | Unix, Python, NGS Library Prep, Capture, Rare Variant Identification |
A nod to the past
I think it important to acknowledge a great deal of help with creating these web pages and materials from previous instructors of the Intro to NGS Bioinformatics course taught in 2013 and the Genome Variant Analysis Course taught in 2014-2016. Two individuals warrant special mention, the former director of the GSAF Scott Hunicke-Smith, and Jeffrey Barrick were the driving force behind this class for a number of years, and many of the tutorials presented here were originally developed by them or adapted from their work.
Verifying setup/access week of June 7th:
In order to ensure as smooth an experience as possible, the week prior to the course, each participant needs to:
- Log into TACC.
- Provide their TACC ID to Dan.
Depending on your operating system you should complete either the window or mac tutorial below. If you are having difficulties be sure to email Dan so a zoom session can be scheduled, and avoid having to use class time on administrative things that may not be resolved without additional help from people at TACC who will not be present in the class.
Windows10
MacOS
Course Schedule
Monday, June 14th. Day 1 – "The Basics"
Presentation: General Course Introduction
Tutorial: Introduction to linux and stampede2
Presentation: Experimental Design
Tutorial: Evaluating raw sequencing data
Tuesday, June 15th. Day 2 – "Principles of Variant calling"
Day 1 catch up and environment verification
Presentation: Read Mapping
Tutorial: Using Bowtie2 to map reads
Presentation: Single Nucleotide Variant Calling
Presentation: Structural Variant Calling
Tutorial: Using samtools to identify SNVs
Tutorial: Using SVDetect to identify SV
Bonus Presentation: Read Mapping Details and File Formats
Wednesday, June 16th. Day 3 – Visualization and User specific tutorials
Presentation: Errors: Where do they come from and how do we identify them as noise rather than signal?
Bonus Presentation: Alternative Library Prep Methods - for when errors really do matter.
Tutorial: Visualization: Integrated Genome Viewer Tutorial
Tutorial: Visualization: Bacterial genome variants the easiest way – breseq
At this point in the course, you have the basic tools that will help you regardless of what type of research you are involved in. The remainder of the course is full of topics that are more specific to different research areas. They are divided into broad categories to help you decide which ones you want to complete during the remaining time. If you are unsure just ask and I'll help identify ones which may be more applicable to your work.
Bacterial Centric Tutorials
Tutorial: Advanced Breseq
Tutorial: breseq with multiple references
Tutorial: Evaluating Error Correction Using Breseq
Human and Higher Eukaryote Centric Tutorials
Tutorial: Human Trios Analysis
Tutorial: Analyzing Annovar Analysis Output
Tutorial: Comparing Multiple samples
Tutorial: GATK
Method based Tutorials that may be of help regardless of sample type
Tutorial: MultiQC - fastQC summary tool for multiple samples
Tutorial: Read processing with trimmomatic
Tutorial: Genome Assembly
Tutorial: Novel DNA identification
Tutorial: Advanced mapping
Tutorial: Error Correction (Molecular Indexing)
Friday, June 18th. Day 5 – User specific tutorials (continued) and TACC the normal way
The first half of today's class will be done as a continuation of tutorials that you are most interested in. As was the case yesterday, choose your own tutorial, and please don't hesitate to ask what tutorials would be good for you to be working on given your data! After the break, we will be go over a brief review to put things back in prospective and give you a tutorial on how to do things the 'normal way' on TACC which means using the job submission system and commands files before giving you any remaining time to go through tutorials and ask any remaining questions.
