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What will be covered?

This workshop covers modern high throughput sequencing technologies, applications, and ancillary topics, including:

  • Illumina HiSeq / MiSeq, and PacBio RS technologies
  • Read Quality Assessment & Improvement
  • Genome assembly
  • SNP and indel discovery
  • RNA-Seq differential expression analysis
  • Experimental design
  • Hardware and software considerations
  • Cloud Computing

We will present a rich collection of lectures and hands-on sessions, covering both theory and tools. This will touch on the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises, which will be performed using the Unix command line on the Amazon Cloud (http://aws.amazon.com/). Exercises will offer the chance to explore software and protocols for high throughput data analysis.

What will I learn? This workshop will prepare you to work independently on basic analyses, using your own computing resources or publicly available on-demand computation, such as AWS.

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … Although here are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis, it is strongly recommended that participants have basic familiarity with the Linux/Unix (or Mac) command line.  Those without command line experience are encouraged to look at our Galaxy workshop in September.

What do I need to bring? … This workshop will be held in a computer room on the UC Davis campus, which has desktop computers running Microsoft Windows OS.  However, if you wish to bring your own laptop to use, you may do so.  We will send out specific software requirements prior to the workshop.

Can I bring my own data? … Yes, you can BYOD! We will be providing small experimental datasets for use during the workshop, but you are welcome to work on your own data as well. If you plan to upload large datasets, please contact us ahead of time

How  much does it cost? … The registration fee is $1,500 for academic, government or non-profit participants and $1,800 for other participants. Amazon has kindly provided grants of $100 per participant for Amazon Web Services accounts. This will allow you to perform analyses during and after the course using Amazon’s resources, without purchasing your own high performance computing servers! Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Where is the workshop? … It will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated.  Attendance is limited to 36 participants in order to foster an effective learning environment and ensure sufficient one-on-one attention.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible once registration opens to ensure your place in the workshop

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