====== 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 [[https://epubs.siam.org/doi/epdf/10.1137/0201010 | Tarjan, 1972]] & [[https://academic.oup.com/bioinformatics/article/23/2/156/205631?login=true | 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  | {{ :teaching:2020summer:compan:bbw089.pdf  | Computational pan-genomics: status, promises and challenges }} |
|  3  | Lisa | [[ https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-016-0066-8.pdf | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage ]] |
|  4  | ALL (Malte)  | [[ https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-020-02135-8.pdf | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs ]] |
|  5  | ALL (Louisa)  | [[ https://www.biorxiv.org/content/10.1101/234856v1.full.pdf | Sequence variation aware genome references and read mapping with the variation graph toolkit ]] |
|  6  | ALL (Jamie)  | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]] |
|  7  | ALL (Lisa)  | [[ https://academic.oup.com/bioinformatics/article/35/19/3599/5372677 | Bit-parallel sequence-to-graph alignment ]] |
|  8  | Louisa  | [[ https://www.biorxiv.org/content/10.1101/2020.01.21.914168v1.full.pdf | BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs ]] |
|  9  | Jamie  | [[ https://link.springer.com/content/pdf/10.1186/s13015-020-00164-3.pdf | Alignment- and reference-free phylogenomics with colored de Bruijn graphs ]] |
|  10  | Malte  | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] |


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