You are here: home » teaching » 2022winter » compan

Computational Pangenomics

M.Sc. Tizian Schulz
Seminar: Wednesday, 10.15-11.45 in U10-146
Office hours: by arrangement
Office: U10-141

Contents

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.

Timeline

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

Topics

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.

Slot Student Paper
2 Tizian Computational pan-genomics: status, promises and challenges
3 Lisa Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
4 ALL (Malte) Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs
5 ALL (Louisa) Sequence variation aware genome references and read mapping with the variation graph toolkit
6 ALL (Jamie) Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
7 ALL (Lisa) Bit-parallel sequence-to-graph alignment
8 Louisa BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs
9 Jamie Alignment- and reference-free phylogenomics with colored de Bruijn graphs
10 Malte Viral quasispecies reconstruction via contig abundance estimation in variation graphs

Back to Teaching