Next Generation Sequencing Workshop
March 10 - April 21 2010

We are pleased to announce a workshop on the topic of next-generation sequencing, organized jointly by the Computational Biology Service Unit (CBSU), the Center for Vertebrate Genomics (CVG), and the Cornell Center for Comparative and Population Genomics (3CPG), and open to members of CVG and 3CPG laboratories.  

The workshop will be held in six weekly sessions, Wednesdays from 3:30-5:00 PM, starting March 10 and running through April 21 (Riley Rob 125).  The emphasis will be on practical, hands-on training in next generation sequencing technologies and associated bioinformatics analysis.

The workshop will have two components:

(1) a series of 1 1/2 hour presentations, in most cases consisting of back-to-back ~40 minute presentations by instructors with specialized knowledge of the topic in question;

(2) an optional practicum in which participants work through detailed exercises with sample data sets, on their own time, using servers at the Cornell Center for Advanced Computing (CAC).  There will be no registration fee for the presentations, but the practicum will have a small fee, to cover the costs of storage and server access at the CAC.  Participants in the practicum will need to establish CAC accounts with a minimum of 50GB storage space (which may be shared among the members of the same research group) and 50 hrs of CPU use. CAC will offer an orientation meeting on March 4th (noon-2pm in Carpenter Engineering Library, ACCEL classroom) covering the basic use of the CAC resources and opening a CAC account. For more information about signing up for CAC account, current rates and CAC user documentation please refer to CAC web site. Participants can sign for the CAC orientation meeting on the workshop registration page.

Workshop Outline  

For more details about workshop sessions, workshop materials, links and instructions for practical exercises please click on each week's link below. The links will be added and updated as workshop materials become available. There is an online discussion forum set up for this workshop.  Workshop announcements will be posted there, and it is the best place to ask any workshop related questions, all teachers and organizers will be monitoring this forum closely. Workshop participants will need to register on forum website to obtain forum id before posting.

Worshop videos are now avaiable for viewing. Access to videos is limited to Cornell users with active Cornell Netid or CBSU registered users authorized to view videos. Videos can be accessed from this page.

Week 1 (3/10):
Overview of next-generation sequencing platforms and applications.  Will include discussion of related technologies (seq-cap, multiplexing), error rates and quality control, and an overview of software and computing resources.  

Week 2 (3/17):
Alignment to reference genomes and variant detection. Emphasis will be on the Illumina technology.  Several alternative tools will be presented, and their strengths and weaknesses will be discussed.  

(no session 3/24 due to Spring Break)  

Week 3 (3/31):
Functional genomic applications.  Will include coverage of RNA-seq, ChIP-seq, and GRO-seq.  Case studies will be emphasized.  

Week 4 (4/7):
Desktop applications or online service.  Emphasis will be on providing non-programmers with the tools needed for basic analysis of nextgen sequencing data.  Presentation by company representatives from SoftGenetics and GenomeQuest.
This session will be longer, it will start at 3:00pm and end at 5:00pm.

Week 5 (4/14):
De-novo assembly.  Assembly of genomes and transcriptomes from short-read data.  Will include coverage of both paired-end Illumina reads and 454 reads.  Various tools will be discussed.

Week 6 (4/21):
Miscellaneous topics, based on feedback from participants. See Week 6 session page for detailed agenda.   

Workshop instructors will include: Qi Sun (Computational Biology Service Unit), Jaroslaw Pillardy (Computational Biology Service Unit), Peter Schweitzer (DNA Sequencing and Genotyping Core Facility), Zhangjun Fei (Boyce Thompson Institute), Josh Waterfall (Lis Lab), Charles Danko (Siepel Lab), Tristan Lefebure (Stanhope Lab), Lalit Ponnala (Computational Biology Service Unit).

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