Genomics
Genomics teaches data management and analysis for genomics research including:
- best practices for organization of bioinformatics projects and data,
- use of command-line utilities to connect to and use cloud computing and storage resources,
- use of command-line tools for data preparation,
- use of command-line tools to analyze sequence quality and perform and automate variant calling.
Dates for the next Genomics workshop will be finalised shortly.
Target audience
- Learners who have completed the Prenomics Course
- PhD Students & Researchers
- This course would be appropriate for learners with experience using the command line, who are expecting to generate a dataset in the future or those who already have a dataset and would like guidance on how to analyse it.
Registration
There are 30 places available for this online workshop, please register using the [online form]. This course is free of charge.
Pre-requisites
Knowledge: learners should have completed the Prenomics course or be able to successfully complete the self-assessment quiz. Learners are also expected to have some familiarity with biological concepts, including the concept of genomic variation within a population. Software: view the required software set-up.
Programme
| Monday | 10:00 - 13:00 | Session 1 - Project management for cloud genomics |
| • Learn how to structure your data and metadata • Plan for an NGS project • Learn about the benefits of cloud computing |
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| Wednesday | 10:00 - 12:30 | Session 2 - Data preparation and organisation |
| • Learn how to automate commonly used workflows • Organise your file system for a new project • Use command-line tools for quality control. |
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| Monday | 10:00 - 13:00 | Session 3 - Assessing read quality; trimming and filtering reads. |
| • Trimming and filtering • Learn how to filter out poor quality data • Assessing read quality |
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| Wednesday | 11:00 - 14:00 | Session 4 - Finding sequence variants |
| • Understand the steps involved in variant calling • Describe the types of data formats encountered during variant calling • Use command line tools to perform variant calling • Instructors will give a demonstration on how to use the Integrative Genomics Viewer (IGV), an interactive tool for the visual exploration of genomic data. |
Learning outcomes
Following completion of this course, learners will be able to
- structure their data and metadata and plan for an NGS project
- organise and document genomics data and bioinformatics workflows
- understand what information is needed by a sequencing facility
- gain practice navigating file systems, creating, copying, moving, and removing files and directories
- use command-line tools to assess read quality and perform quality control
- align reads to a reference genome, and identify and visualise sequence variants
- work with Amazon AWS cloud computing and transfer data between a local computer and cloud resources
Scholarships
We offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.
The scholarship scheme can cover approximately £150 per application, for costs such as:
- childcare
- accessibility needs
- other costs that might otherwise prevent participation
- second monitors and headsets.
You will need to reclaim these expenses by completing a form and submitting receipts after participation in the course.
To request a scholarship please indicate this in the registration form, before the given deadline. Submissions after this date will not be considered. We will contact you one week after the deadline to confirm whether you have been awarded a scholarship.