Last modified: 31 May 2022 13:05
An exciting course that brings a student right up to date with bioinformatics, genome assembly and annotation technology. You, the student, will analyse the genome of an unknown bacterium from the environment. The genome of this isolate has been extracted and whole genome sequenced. You will then assemble your own bacterial genome and functionally annotate it, taught by expert bioinformaticians from our Centre for Genome-Enabled Biology and Medicine. Your analysis will enable you to identify the species you have isolated, its metabolic and environmental responses, growth constraints and regulation, cell surface markers and antibiotic resistance, producing a full inventory of genes and their presumptive functions. Overall, the course prepares a student for future employment in a biosciences workplace, where genome sequencing and annotation is becoming an everyday tool of modern biotechnology.
|Session||Second Sub Session||Credit Points||15 credits (7.5 ECTS credits)|
This course will take students through the exciting and challenging process of analysing the sequence of a bacterial genome from an environmental isolate. The course will teach students how to quality filter and trim raw sequencing data, assemble a genome, quality control the output, annotate genes, and carry out functional gene analysis using modern bioinformatics, to produce an assembled genome and full inventory of the genes of a novel bacterial isolate. This course will develop your knowledge and skills in bioinformatics analysis of genomic data, and you will learn how to use scripting via the command line and the Galaxy interface.
Information on contact teaching time is available from the course guide.
|Assessment Weeks||34||Feedback Weeks||39|
1 hour exam. Feedback per question with marking.
|Assessment Weeks||35||Feedback Weeks||38|
Feedback per question with marking.
|Assessment Weeks||27,28,29,30,31,32,33||Feedback Weeks||27,28,29,30,31,32,33|
Tutor answers to questions and feedback to comments, as relevant.
|Assessment Weeks||32||Feedback Weeks||35|
1.5 hour exam. Feedback per question with marking.
|Assessment Weeks||27,28,30,32||Feedback Weeks||27,29,31,32|
MCQs on genome assembly process, outputs, and caveats. Marking and feedback during tutorial.
|Knowledge Level||Thinking Skill||Outcome|
|Conceptual||Analyse||Explain the underlying principles of the tools used and analyse your outputs to determine the validity and limitations of the approach and/ or data.|
|Procedural||Apply||Develop skills in Unix and the command line within a HPC infrastructure.|
|Conceptual||Evaluate||Critically evaluate your findings in the context of the field of microbial genomics and the global health challenge of antimicrobial drug resistance.|
|Conceptual||Evaluate||Demonstrate knowledge by explaining and critically appraising through written presentation appropriate to specialists in the field of genomics.|
|Procedural||Create||Apply and enhance these informatics skills to perform analysis of a genomics dataset (next generation sequencing data) using bioinformatics software to assemble a bacterial genome and identify ARGs.|