Half-day workshop on Genome Assembly, Annotation, and RNA-Seq


Dec 2, 2015     1:00 PM – 4:00 PM EDT


REGISTER to attend in person or online

This half-day workshop introduces a variety of free bioinformatics tools and resources for dealing with genome datasets – including assembly, annotation, RNA-Seq. Using cyberinfrastructure (CI) developed by the iPlant Collaborative, attendees will learn how to upload and share any genomic dataset and conduct analyses through web (Discovery Environment) or cloud/Linux command-line (Atmosphere) interfaces. The session is an opportunity for existing users to get up-to-date on iPlant’s newest features (e.g. tool integration with Docker, Data Commons, and Agave API). Training provided will help new users to further explore iPlant tools for GWAS, methylation studies, image analysis, and more. While many examples will focus on plant data, iPlant resources are equally useful for all domains of life.

Key topics and examples covered include:

  • Managing and sharing large datasets
  • Best practices and new technologies in Genome Sequencing and Assembly
  • Genome annotation with the MAKER pipeline
  • Overview and new methods for RNA-Seq (from Tuxedo to Kallisto)

iPlant platforms accommodate every level of user – from “bench-biologist” to bioinformatician and computational resources include generous storage allocations as well as access to cloud and high-performance. iPlant platforms are extensible and customizable via application programming interfaces (APIs)/ RESTful services, and web-based systems for data access, tool integration, and analysis. Training and online learning materials provide support for collaboration and people – helping all users get started with iPlant.

How to attend/What to bring:

Please obtain a free iPlant account and register for the workshop. The workshop is free and in-person attendees (registration limited to 30) will also receive complimentary lunch and coffee. Please bring a Wi-Fi enabled laptop to the session. We will send pre-workshop prep materials to all registered attendees. Please bring a Wi-Fi enabled laptop to the session. Pre-workshop prep materials will be sent to all registered attendees.

Can’t make it in person:

Register for the livestream – you and interested colleagues can register to watch – see link above. Recording will be available shortly after the program.

iPlant is funded by the National Science Foundation (#DBI-0735191), iPlant is driven by and freely available to the community.

Location: Cold Spring Harbor, NY

Primary Contact: Jason WilliamsiPlant Collaborative

(find out more…)

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