Half-day workshop on bioinformatics tools for Plant Genomics

Nov 29, 2017     12:00 PM - 5:00 PM Eastern



REGISTER to attend in person or online


Prior to the start of the CSHL Plant Genomes Meeting, a half-day workshop will be sponsored by the Gramene (NSF #1127112) and CyVerse (NSF # 1265383) projects and will cover public bioinformatics tools and resources for dealing with genome datasets including new technologies in genome sequencing and assembly, fast and efficient methods for RNA-Seq analysis, and data submission to public repositories such as TrackHub. Lunch and coffee will be included.


Key topics and examples covered include:

  • Storing, managing and sharing large data sets

  • Best practices and new technologies in genome sequencing and assembly

  • Genome annotation tutorial with the MAKER pipeline

  • RNA-Seq tutorial including new fast and efficient methods (e.g. Tuxedo 2.0 and Kallisto)

  • Data submissions to public repositories such as TrackHub, Atlas and the European Variation Archive with the resulting data visualization in Gramene’s genome browser


Hands on tutorials and short lectures will get users started using these tools, resources, and databases right away. While some familiarity with with command line is beneficial, the majority of exercises will make use of easy-to-use web-based interfaces, including the CyVerse Discovery Environment, Gramene Databases, and CyVerse SciApps workflows.



Please obtain a free CyVerse account. 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.



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

CyVerse and Gramene are funded by the National Science Foundation (#DBI-1265383 and #IOS-1127112, respectively).  Gramene is also partially by the USDA-ARS (1907-21000-030-00D).  Our resources are driven by and freely available to the community.

Cold Spring Harbor, NY
Primary Contact: 

Jason Williams - CyVerse

End date: 
Wednesday, November 29, 2017 - 16:00