Broad/Illumina Genome Analyzer Boot Camp

This course contains narrated presentations and video-based lab modules from the Genome Analyzer Boot Camp developed jointly by The Broad Institute and Illumina and held in February 2010. In this online version of the Boot Camp sessions, you’ll get an in-depth look at the chemistry and workflows for the Genome Analyzer. You’ll learn tips and tricks as well as best practices developed by the Broad to achieve even higher performance from the Illumina Genome Analyzer.

This course is intended for technician-level individuals who have some wet lab experience with the Illumina Genome Analyzer and corresponding sample prep techniques. The video sessions will take approximately 3 hours 25 minutes to complete.

We welcome any feedback on the course, and would also love to hear about the things that you are doing in your labs! For more information about GA Boot Camp, or to provide feedback, please email

Course Content

Sample Prep    
Videos and Slides View Download
Illumina – Sample Preparation (Chemistry) [ video ] [ slides ]
Broad – Sample Preparation (Tracking, Shearing, Diversity, Size Selection, SPRI) [ video ]  
Lab 1a Video [ video ]  
Lab 1b Video [ video ]  
Posters (from Lab 1a Video)
Agilent Bioanalyzer considerations   [ poster ]
Effects of Covaris Shearing Factorial settings   [ poster ]
Cluster Generation    
Videos and Slides    
Illumina – Cluster Generation (Chemistry) [ video ] [ slides ]
Broad – Cluster Generation (QPCR, Controls, SYBR QC) [ video ]  
Lab 2 Video [ video ]  
Videos and Slides    
Illumina – Sequencing (Chemistry) [ video ] [ slides ]
Broad – Sequencing (Workflow, 1st base, Failure Mode Gallery) [ video ]  
Lab 3a Video [ video ]  
Lab 3b Video [ video ]  
Illustrations (from Lab 3a Video)    
Sequencer stage set-up   [ illustrations ]
Data Analysis    
Videos and Slides    
Illumina – Working with Data (Pipeline workflow) [ video ] [ slides ]
Broad – Working with Data (Troubleshooting, Data files, Concepts) [ video ]  
Lists and Data Process Map    
List of Acceptable Metrics   [ list ]
Troubleshooting Data Process Map   [ map ]
List of File Locations   [ list ]

Sample Prep: Karen Israel, Maura Costello, Laura Lambiase, Purnima Kompella, Brian Minie, Jillian Nolan
Cluster Generation: Karen Israel, Tim Desmet, Matt Coole, Laurie Holmes, Adam Navidi
Sequencing: Klaus Ullman, Sheridon Channer, Amy Biasella, Dalin Chan, Paul Frere, Sheridon Channer, Mike Monahan
Data Analysis: Klaus Ullman, Kristen Connolly, Amy Biasella, Jim Meldrim

Created by the Boot Camp Team at the Broad Institute1 and Illumina2:
Kristen Connolly1, Sheila Fisher1, Steve Becker2, Maura Costello1, Amy Biasella1, Sheridon Channer1, Laura Lambiase1, Purnima Kompella1, Brian Minie1, Jillian Nolan1, Justin Abreu1Tim Desmet1, Matt Coole1, Laurie Holmes1, Adam Navidi1, Dalin Chan1, Paul Frere1, Ryan Hegarty1, Jim Meldrim1, Danielle Perrin1, Mike Monahan2, Erin Wheatley2, John Pinter2, Scott Brazinski2, Kimberly Roadinger2, Elizabeth McCroskey2