course materials, Online material, Training materials
Cloud-SPAN Genomics
Genomics teaches data management and analysis for genomics research including: (1) best practices for organization of bioinformatics projects and data, (2) use of command-line utilities to connect to and use cloud computing and storage resources, (3) use of command-line tools for data preparation, (4) use of command-line tools to analyze sequence quality and perform and automate variant calling.
The module is designed for a four half-day, tutor-led workshop, or for self study.
DOI: https://doi.org/10.5281/zenodo.6564314
Licence: Creative Commons Attribution 4.0 International
Keywords: Shell, Command line, Cloud computing, Genomics, HPC, Data analysis, Bioinformatics, High performance computing
Target audience: Graduate students, Students, Biologists, PhD Students, Post docs
Resource type: course materials, Online material, Training materials
Version: 1.0
Status: Active
Prerequisites:
We have found that people taking the Genomics module can vary the amount of experience they have had in navigating file systems and using the command line. We have designed another module, Prenomics, to prepare those with less experience for Genomics. We have a Self-assessment Quiz to help you decide if you would benefit from Prenomics before the Genomics module. The Prenomics module assumes no prior experience and is designed for absolute beginners.
Learning objectives:
(1) best practices for organization of bioinformatics projects and data, (2) use of command-line utilities to connect to and use cloud computing and storage resources, (3) use of command-line tools for data preparation, (4) use of command-line tools to analyze sequence quality and perform and automate variant calling.
Date created: 2022-03-31
Date published: 2022-10-18
Contributors: James Chong, Emma Barnes, University of York, Software Sustainability Institute
Scientific topics: Bioinformatics, Software engineering, Genomics, DNA polymorphism, Workflows, Data architecture, analysis and design
Activity log
