M.Sc. Tizian Schulz
Seminar: Wednesday, 10.15-11.45 in U10-146
Office hours: by arrangement
Office: U10-141
Based on original research papers, the participants will give oral presentations (20-45 min, optimally about 25 min's) and write short summaries (ca. 5 pages), both in English, about current algorithmic problems in computational pangenomics and their solutions. Deadline for the written summary is one week after the presentation.
12.10. | Preliminaries, topic selection | Tizian |
19.10. | Computational pan-genomics: status, promises and challenges | Tizian |
26.10. | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage | Lisa |
02.11. | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs | ALL (Malte) |
09.11. | Bifrost (continued) | ALL (Malte) |
16.11. | Sequence variation aware genome references and read mapping with the variation graph toolkit (see also Tarjan, 1972 & Farrar, 2007) | ALL (Louisa) |
23.11. | (Tizian away) | |
30.11. | (Tizian away) | |
07.12. | (Tizian away) | |
14.12. | (Tizian away) | |
21.12. | (Tizian away) | |
11.01. | Bit-parallel sequence-to-graph alignment | ALL (Lisa) |
18.01. | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs | Louisa |
25.01. | Alignment- and reference-free phylogenomics with colored de Bruijn graphs | Jamie |
01.02. | Viral quasispecies reconstruction via contig abundance estimation in variation graphs | Malte |
The topic of the talk/report should be recent algorithmic problems in computational pangenomics and their solutions.
The students are encouraged to suggest their own topics.
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