BIOINF4362 Seminar Algorithms in Bioinformatics - Advanced Sequence Analysis
| Lecturer | Dr. Monika Balvočiūtė and Prof. Dr. Daniel Huson |
| Venue | Thursdays, 12:15-14:00, Kleiner Hörsaal, Sand 6/7 |
| Signup | Send email to: Dr. Monika Balvočiūtė |
| Start | 27-Oct-2015 |
| Links | Campus |
| Language | English |
The topic of this seminar will be algorithms and applications in advanced sequence analysis.
Schedule
| Date | Topic | Student | Tutor |
|---|---|---|---|
| 24.11. | Quality of an assembly. QUAST: quality assessment tool for genome assemblies. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies | ||
| 24.11. | Haplotype assembly. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads | ||
| 1.12. | Long read assembly. Genome assembly using Nanopore-guided long and error-free DNA reads. Genome assembly from synthetic long read clouds. | ||
| 1.12. | Taxonomic profiling. Metagenoic microbial community profiling using unique clade-specific marker genes | ||
| 8.12. | Read assembly and metagenome assembly. Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies. Ray Meta: scalable de novo metagenome assembly and profiling. | ||
| 8.12. | Genome compression. Trends in genome compression. QVZ: lossy compression of quality values. How DNA could store all the world’s data. | ||
| 15.12. | Suffix array construction. A bioinformatician’s guide to the forefront of suffix array construction algorithms. | ||
| 12.1. | Variant analysis. Best practices for evaluating single nucleotide variant calling methods for microbial genomics. A survey of tools for variant analysis of next-generation genome sequencing data. A framework for variation discovery and genotyping using next-generation DNA sequencing data. A global reference for human genetic variation. | ||
| 12.1. | Functional profiling. g:Profiler––a web server for functional interpretation of gene lists (2016 update) Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies | ||
What is expected of you in this course:
We provide the title of one or two papers that provide a pointer to the topic. Please survey the literature to find more papers on your topic. Develop an outline of what you think would like to cover in your presentation. Discuss your outline with one of the lecturers for this course. Arrange to meet one week before your talk with one of the lecturers to show them your finished presentation and writeup. Failure to be prepare your presentation and writeup by this deadline will have a negative impact on your grade, regardless of how good the presentation is... Your presentation should be 25 minutes long. It will be followed by a discussion and you should be prepared to answer questions on your topic. Your writeup should present the topic in your own words. Please format it as a scientific article, with title, author, abstract, figures, citations etc. Please clearly any text or figures that you did not create yourself. For figures, both in your paper and your presentation, have an explicit citation right next to the figure, something like: Image source: Altschul et al, 1990. The aim of your presentation is to efficiently communicate something of interest to the other participants of the course. Make sure that you have an interesting story presented in a user-friendly way. Your grade will be based on your presentation. You must hand in an adequate writeup to pass the course. A very good writeup will improve your grade, whether a poor writeup will have a negative effect on your grade.