Next Generation Sequencing Workshop
March 10 - April 21 2010

Week 1 (March 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.

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.

The speakers will be available to answer questions for this session on Friday March 12 from 3:00 to 4:00 PM in 102 Weill (small conference room).

Week 1 data files:
            public directories ftp://cbsuftp.tc.cornell.edu/ngw2010/session1
            protected directories ftp://usr@cbsuftp.tc.cornell.edu/ngw2010p/session1
NOTE: User id and password to access protected files have been e-mailed to registered participants. Replace "usr" in the link above with the user id you received.

Lecture 1.  The instruments, the runs, the QC metrics, and the output
Speaker: Peter Schweitzer (DNA Sequencing and Genotyping Core Facility).

 

Lecture 1 slides.

 

Roche/454 GS-FLX

•  454 (GSRunbrowser information)                        

  •  Evaluating run results

•  Errors produced

•  Data files that are produced and distributed

Illumina/Solexa

• Types of runs available

• Evaluating run results

•  Summary stats page, error graphs, images            

•  Errors produced            

•  Data files produced and distributed

Both platforms

• Multiplexing options            

• Sequence capture technologies                        

  • Nimblegen and other microarray-based                        

  •  Agilent bead-based                        

  • Raindance Technologies PCR-based

 

Lecture 2.  Working with the data files.

Speaker: Qi Sun (Computational Biology Service Unit).

 

Lecture 2 slides.

• What these data files represent: an in-depth look into the FASTQ  and SFF files

• Error distribution and quality scores in both platforms

• Using FASTX toolkit for QC,  trimming and de-multiplexing of Solexa data            

• Introduction to the Roche 454 Software package            

• Computational resources at Cornell.  

 

Exercise:

Download exercise instructions here.

1. Use FASTX toolkit to generate report of data quality, and do quality trimming

2. Use 454 GSMapper to align reads to E.coli genome, and inspect the flowgram intensity and base calling errors.

 

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