Teaching materials for the London School of Hygiene and Tropical Medicine Parasite Genomics modules for 2023.
Instructors:
- Adam Reid, Gurdon Institute, University of Cambridge
- Stephen Doyle, Parasites & Microbes Programme, Wellcome Sanger Institute
- Thursday 27th April
- 9:30-12:45: Computer Practical 1: Viewing genome sequences (Artemis)
- 14.00-17.00: Computer Practical 2: Sequence variants (Mapping short reads)
- Friday 28rd April
- 9:30-12:45: Computer Practical 3: Comparative genomics
- 14.00-16:45: Computer Practical 4: Transcriptome analysis (RNA-seq 1)
- 16:45-17:15: First week Q&A discussion with module organisers
This course aims to give you experience in using software to analyse genomic DNA to address biological questions. The software will include downloadable graphical user interface (GUI), web-based, and UNIX-based command line tools. Using the command line can and will be very new and foreign to many of you, and much like learning any new language, will take time and practice to master. To get you started, we highly recommend you attempt the Introduction to Shell tutorial available at DataCamp, which you can access using the link below. In doing so, you will have a significant advantage in the modules that require you to use the command line.
You will need to sign up for an account, however, this tutorial is free. There are many other tutorials, some are free and some require a subscription, that may help you with difference aspects of data analysis, so please do check them out.
DataCamp - Introduction to Shell
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Computer Practical 1: Viewing genome sequences
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Computer Practical 2: Analysis of sequence variants
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Computer Practical 3: Comparative genomics
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Computer Practical 4: Transcriptome analysis
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Appendix
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Comparative genomics of apicomplexans – with a focus on large gene families (Adam Reid): Video lecture, Slides
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Comparative genomics of helminths (Stephen Doyle); - Video lecture - Slides