Genome Assembly and Introduction to Annotation
This course will provide students with essential bioinformatics skills for high-quality genome assembly and analyses. Through lectures, demonstrations, and hands-on exercises, students will learn to initiate genome projects and critically evaluate publicly available genome data to address their scientific questions. Key topics include working with short and long reads, read quality assessment, estimating genome size, heterozygosity and repeat content using k-mer methods, genome assembly, and Hi-C for genome scaffolding. Students will also explore genome quality assessment with BUSCO, merqury, Hi-C curation, read mapping and annotation using RNA-Seq and tools such as BRAKER3. Emphasis will be placed on both understanding the theory and developing data analysis skills.
The course will be offered for the first time in March 2025 (will run again in September 2025 and March 2026 before Prof II contract ends). It will run as a intensive one-week course. About half the time will be devoted to lectures, and the other half to exercises. Lectures and exercises are 40 hours in total. Self-study and exam preparation (software installation, theory of genome biology, paper reading, analyzing data, preparing report) is estimated 150 hours. The total workload is thus 190 hours.
Requirement of 15 ECTS within the field of genetics/genomics/molecular biology. Examples of courses that can fulfill this requirement:
BIO2011 Genomics and Bioinformatics
BIO2009 Molecular Cell Biology
BIO1013 Evolution and Genetics
BIO2015 Molecular Ecology
Courses from other universities may fulfill the requirement upon application.
Knowledge:
- In-deph understanding of topics, theories, processes tools and methods used for high-quality chromosome-level genome assembly, annotation and initial whole-genome analyses
Skills
- Have aquired the skills to conduct genome assembly projects, including handling whole-genome-sequencing data (short and long reads)
- Performing genome assembly (with different softwares), and scaffolding with Hi-C
- Performing evaluation of genomes assembled: BUSCO completeness, kmer completeness (merqury), contamination checking
- Develop the ability to critically evaluate the quality of various genome assemblies (from drafts to complete), and understand the biases these may introduce into subsequent molecular analyses
- Have aquired basic skills to use Unix command-line
General competencies:
- Be able to innitiate and conduct genome assembly projects with the latest state-of-the-art algorithms and methods
- Gain the ability to perform comprehensive whole-genome analyses using both self-generated and publicly available data from diverse sources.
- Develop the ability to engage with molecular biologists and genomicists at the highest level, discussing state-of-the-art standards in genomics and contributing to the field by producing high-quality genomic resources and conducting downstream analyses
At campus. Block teaching. Preparatory work, initiated around three weeks before the start of the course.
A series of lectures, seminars, demonstrations and hands-on computer laboratories that cover theory and practice of genome assembly and analyses.
Compound assessment (SV):
Mandatory exercises (OD): approved / not approved
Assignment/report (OP): counts 100 %, A-F
The evaluation will be report-based. Students will undertake a mini-genome assembly project, from read quality assessment to Hi-C scaffolding, using either their own data or data provided by Prof. Uiano-Silva. They will critically assess the quality of the assembly and document the process and results in a report, which must be submitted within one month after the course concludes. The report format of Introduction, Methods, Results and Discussion will be encouraged.
Before and after the course, there will be remote office hours where students can seek assistance with software installation, report-related questions, or discuss their genomics-related master's or PhD projects. During this time, students will work independently to complete their reports, but are adviced to schedule at least one remote meeting with course coordinator before submitting their reports.