Thank you for your interest in participating in this Cloud-SPAN workshop. Below you will find answers to some frequently asked questions about this curriculum. If the answer to your question doesn’t appear below, please contact cloud-span-project.york.ac.uk or open an issue in one of our Github repos.
What does this workshop cover?
This workshop teaches data management and analysis for genomics research including: best practices for organization of bioinformatics projects and data, use of command line utilities, use of command line tools to analyze sequence quality and perform variant calling, and connecting to and using cloud computing.
What experience do learners need to have before this workshop? What will they be able to do by the end of the workshop?
This lesson assumes no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. By the end of the workshop, learners will be able to:
- structure their metadata, and organize and document their genomics data and bioinformatics workflow;
- navigate their file systems, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards;
- use command-line tools to perform quality control, align reads to a reference genome, and identify and visualize between-sample variation;
- work with Amazon AWS cloud computing and transfer data between their local computer and cloud resources.
What are the software, hardware, and connectivity needs for this workshop?
Learners will need to bring a laptop (not a tablet). Learners using a Windows machine will also need to download and install Git Bash. There are no other hardware or software requirements. Learners will need a stable, strong internet connection in order to work on the remote computing system used for this workshop and participate in the online video call.
My institution has its own compute cluster, or our research group uses a different cloud computing resource. Can we deliver the workshop using that system?
This course is based on a genomics workshop developed by The Carpentries. To ensure a consistent workshop experience for learners and Instructors, all workshops organized by The Carpentries (“centrally-organized workshops”) use a stable, community-tested curriculum and technical set-up. We have adapted this curriculum and setup to suit our and our users’ needs. Currently, this means all our Genomics workshops are taught using Amazon Web Services, although we may be interested in supporting other systems in the future.
Where can I find more information about this workshop?
For a full description of this workshop, including what content is covered, and what dataset we use to teach, visit the Genomics Workshop Overview page.