Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.
Refgenie is a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.
Research Computing can help with accessing, preparing, visualizing and analyzing data. We can assist you by implementing your analysis strategy in an appropriate computing language, including R, Python and Matlab. We will work with you to prepare scripts that are reproducible, efficient and flexible.
Manipulation Data analysis generally involves a significant effort to transform, aggregate, subset or otherwise prepare a dataset. That could include dealing with missing values as well as merging or joining multiple datasets. We can help you wrangle your data into a “tidy” format in order to analyze the features and observations relevant to your question.
UVA Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by experts and are freely available to UVa faculty, staff and students.
Upcoming Workshops Workshops for 2021 have been moved to online learning formats due to campus closures from COVID-19.
DATE WORKSHOP INSTRUCTOR 01/19/2021, 01/20/2021, 01/21/2021 High Performance Python Katherine Holcomb 02/04/2021 Introduction to Shiny Christina Gancayco 02/05/2021, 02/12/2021 Parallel Matlab Ed Hall 02/11/2021 Customizing Shiny Apps Christina Gancayco 02/12/2021 Optimizing R Code Jacalyn Huband 02/18/2021 Building Containers for Rivanna Ruoshi Sun 02/19/2021 Optimizing Matlab Code Ed Hall 02/25/2021 Minimal Containers Ruoshi Sun 02/25/2021 Biopython Karsten Siller 03/16/2021 Using Bioinformatics tools on Rivanna Gladys Andino 03/12/2021 Parallelizing R Jacalyn Huband 04/09/2021 R with MPI Jacalyn Huband Research Computing is partnering with the Research Library and the Health Sciences Library to deliver workshops covering a variety of research computing topics.