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).