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Day 1: Course Overview, Intro to Illumina and Library QC

Welcome to Day 1 of the Short-Read Sequencing Analysis Workshop. Today we will be going over what this workshop is about, as well as introduce you to Illumina sequencing and some aspects of library QA/QC. We encourage you to watch the videos for Day 1 before the first day of class, but unlike the rest of the workshop these videos can also be watched after the class and you won't be left behind.

Videos for Day 1

Video1: Course overview and Experimental Design (Please note this video was made for the 2014 class so please refer to the information for the 2015 course instead of the video for the syllabus and course structure)

Video2: Introduction to Illumina Sequencing This video goes through some of the basics of how Illumina sequencing works, as well as explaining some of the run statistics that are produced during the sequencing process. 

Here is the Illumina video we suggested you watch that explains the Illumina SBS chemistry in more detail (~5 minutes)

Video3: Library QA & QC This video presents some of the issues researchers face when choosing library prep methods and explains some of the common quality control and quantification methods for completed libraries.

Video4: Overview of computational analysis (This is video 3 from 2014) This video gives a quick overview of computational analysis for short-read sequence analysis.

Slides for Day 1

Day1 In-class slides

Video1 slides

Video2 slides

Video3 slides

Video4 slides


Day1 Homework

 Additional resources and recommended reading

Sequencing Depth and Coverage paper (pdf file) This is a great 2014 Nature Reviews paper that goes over some of the considerations for deciding on sequencing depth for different types of experiments. It discussing everything from cost considerations to what is considered good practice for data analysis.

High Throughput Sequencing Technology review (pdf file) A 2015 Molecular Cell review that goes over the current sequencing technology including Illumina and Ion Torrent, as well as some of the single-molecule technologies from Pacific Biosciences and Oxford Nanopore Technologies.

Library Construction paper (pdf file) A 2014 Biotechniques paper that reviews many different types of NGS libraries.


2014 Course Material