Genome-scale technologies 2 1000-719bTG2
1. Next generation sequencing:
- various sequencing technologies and their output,
- applications: genome resequencing, targeted sequencing (transcriptome, exons, immunoprecipitation), 'de novo' sequencing, 'metagenome' sequencing,
- experiment design and quality control.
2. Algorithmic problems and their typical solutions:
- short read assembly (e.g. de Bruijn graphs),
- read mapping (e.g. Burrows-Wheeler transform, Ferragina-Manzini index),
- genome variation discovery (copy number variation, single nucleotide polymorphism and structural variation discovery)..
3. Differential analysis problems:
- differential gene expression analysis with RNA-seq,
- microRNA and long-non-coding-RNA identification in sequencing data.
Type of course
Learning outcomes
Knowledge:
- typical modern genome-scale technologies
- basic distributions describing genome-scale measures and algorithms to their analysis
Abilities:
- application of proper technology to a given biological problem
- design of genome-scale experiments and its results' analysis
- application of proper statistical model to experiment results
- implementing selected algorithms to experiment result analysis
Competences:
- awareness of own limitations and the need for further education (K_K01)
- awareness of the need for systematic work on software projects (K_K02)
Assessment criteria
Final assesment is based on lab projects and (optionally) oral exam.
PhD students should carry out projects individually.
Bibliography
"Large-scale genome sequence processing", M. Kasahara, S. Morishita, Imperial College Press, 2006
"Bioinformatics for High Throughput Sequencing", N. Rodríguez-Ezpeleta, M. Hackenberg, A.M. Aransay, Springer, 2012
Additional information
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: