58310108 Seminar: Sequence Assembly (3 cr, Spring 2010)
The seminar covers a wide range of topics related to the fascinating interplay of biotechnology and computer science that have made possible the assembly of whole genome sequences. The seminar is especially targeted to students in Master's Degree Programme in Bioinformatics (MBI), but also very suitable for students specializing into algorithms and machine learning or for students with background studies in biotechnology.
Time and place
- Mondays 12-14 C222 (18.01.-22.02.,15.03.-26.04.).
Seminar organizer
- Academy Research Fellow Veli Mäkinen
Enrolling for the seminar
Please use the registration system of the Department of Computer Science to enroll for the seminar.To complete the seminar
Each student
- gives an oral presentation (45 min) from a selected topic,
- writes an essay (10-15 pages) on the same topic,
- participates at least 75% of the seminar sessions.
Schedule
General reading
- Review on mapping and assembly.
- Review on next-generation sequencing technologies
- Review on ChIP-Seq and RNA-Seq tools
Topics / Presentations
- HA: Sequencing technology review: Sanger sequencing,
next-generation sequencing
[Presentation] [Essay] - Sequencing applications: ChIP-Seq and RNA-Seq
- MS: Sequencing puzzle: Sequencing from Compomers: The Puzzle
[Presentation] [The Game] [Essay] - JR: Shortest superstring approximations: (Section 2.3 and Chapter 7 in V. Vazirani: Approximation Algorithms, Springer 2001)
[Presentation] [Essay] - Overlap-layout-consensus -based assemblers: wgs-assembler,...
- AS: de Bruijn graph -based assemblers: Euler, Velvet,
ABySS, SOAPdenovo,...
[Presentation] [Essay] - SH: Hash-based short read mapping methods: MAQ, SOAP, ELAND, SHRiMP, ZOOM,BFAST, MOSAIK (see also PatternHunter and Rasmussen et al. for the core techniques)
[Presentation] [Essay] - NV: Burrows-Wheeler Transform and FM-index -based short read mapping methods: Bowtie, BWA, SOAP2
[Presentation] [Essay] - KP: RNA-Seq mappers: TopHat,
G-Mo.R-Se, QPALMA
[Presentation] [Essay] - AK: Resequencing and haplotyping: Genotype imputation, Local haplotype reconstruction
[Presentation] [Essay] - RK: Resequencing and structural variation detection: Review, Combinatorial approach to structural variation detection, SNP detection (Atlas-SNP2)
[Presentation] [Essay] - RT: ChIP-Seq analysis: review, CisGenome, SISSRs, ...
[Presentation] [Essay] - SP: Metagenomics: Genovo, metagenomics in virology, discovery of new plant viruses,
sequencing vsRNA of plant viruses
[Presentation] [Essay]