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This workshop will cover 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

The course includes a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises. Workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the Amazon Cloud (http://aws.amazon.com/) which allows for powerful web-based data analyses. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data. There are no prerequisites other than basic familiarity with genomic concepts. Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

NOTE: This is a Galaxy-based workshop and therefore will not cover command line training; please consider our September Workshop if you are interested in performing bioinformatics analyses on the command line.

Attendance is limited to 35 participants in order to foster an effective learning environment and ensure sufficient one-on-one attention. Course tuition is $1,500 for academic 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 analysis during and after the course using Amazon’s resources, without purchasing your own high performance computing servers!

The workshop will be held on the UC Davis campus and will run from 9am to 5pm on the dates indicated. Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Schedule

Monday

  • High Throughput Sequencing & Galaxy Fundamentals

Tuesday

  • Alignment & Variant Calling

Wednesday

  • Genome Assembly

Thursday

  • RNA-Seq

Friday

  • Challenge Exercises!
  • Sequencing & IT Issues
  • Wrap-up

06/09/2014 – Registration has been closed.  However, space is currently still available for the September command line version of this workshop.