Update index.qmd

Update text for Genomics

upcoming/Genomics/index.qmd

@@ -1,6 +1,54 @@
 ---
 title: "Genomics"
 image: genomics-card-narrow.png
-description: Learn 
+description: Learn data management and analytical skills for genomic research
 ---
 
+## Registration
+This course is free of charge, however we ask that you register for the Self-Study learning mode using the registration button below, so we have your details and we can provide you with additional information. 
+
+## 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. Please note, you will need to complete the Creating your own instance course beforehand.
+Software: view the required software set-up.
+
+## Programme 
+
+Topics: 		
+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
+Session 2 - Data preparation and organisation
+Learn how to structure your data and metadata
+Plan for an NGS project
+Learn about the benefits of cloud computing
+ 		Session 3 - Assessing read quality; trimming and filtering reads
+Trimming and filtering, learn how to filter out poor quality data
+Assessing read quality
+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. 
+
+|                     |               |                                                                |
+|------------------|------------------|------------------------------------|
+| Monday 15 January 2024 | 10:00 - 13:00 | Session 1 - Project management for cloud genomics  |
+| Wednesday 17 January 2024  | 10:00 - 13:00 | Session 2 - Data preparation and organisation               |
+| Monday 15 January 2024 | 10:00 - 13:00 | Session 3 - Assessing read quality; trimming and filtering reads |
+| Wednesday 25 January 2024 | 11:00 - 14:00 | Session 4 - Finding sequence variants                         |
+
+## 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. 
+
+## 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