====== Computational Pangenomics ====== M.Sc. Tizian Schulz\\ Seminar: Wednesday, 10.15-11.45 in U10-146\\ Office hours: by arrangement \\ Office: U10-141\\ \\ **Important notice:**\\ The seminar will take place as an online course via Zoom. Details for participation can be found at the [[ https://bis.uni-bielefeld.de/sites/27608/Start.aspx | Lernraum ]]. ===== 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. Each week, we cover another aspect of scientific writing and put it into practice. Deadline for the written summary is one week after the presentation. ===== Timeline ===== | 22.04. | Preliminaries, topic selection | | | 29.04. | Intro to LaTeX, reading | {{ :teaching:2020summer:compan:template.tar | latex sources }}, {{ :teaching:2020summer:compan:reading.pdf | Slides: HowToRead }} | | 06.05. | Scientific writing | {{ :teaching:2020summer:compan:scientificwriting.pdf | Slides: ScientificWriting }}, [[ https://de.sharelatex.com/learn/bibtex_bibliography_styles | Bibliography Styles ]] | | 13.05. | Introductions, conclusions | {{ :teaching:2020summer:compan:introsconclusions.pdf | Slides: IntroductionConclusions }} | | 20.05. | Math | {{ :teaching:2020summer:compan:math_template.tar | latex sources }}, {{ :teaching:2020summer:compan:math.pdf | Slides: Math }} | | 27.05. | Tables, figures, algorithms | {{ :teaching:2020summer:compan:algo_template.tar | latex sources }}, {{ :teaching:2020summer:compan:tablesFiguresAlgos.pdf | Slides: TablesFiguresAlgorithms }} | | 03.06. | Checklist, writing | {{ :teaching:2020summer:compan:checklist.pdf | Slides: Checklist }} | | 10.06. | Intro to presentations (in LaTeX Beamer) | {{:teaching:2020summer:compan:beamer_template.tar | latex sources }}, [[ http://texdoc.net/texmf-dist/doc/latex/beamer/beameruserguide.pdf | beamer class doku ]], {{:teaching:2020summer:compan:checklist_presentations.pdf | Slides: Presentation Checklist }} | | 17.06. | presentations (1) | | | 24.06. | presentations (2) | | | 01.07. | presentations (3) | | | 08.07. | presentations (4) | | | 15.07. | presentations (5) | | ===== 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 }} | | | | [[ https://almob.biomedcentral.com/track/pdf/10.1186/s13015-016-0066-8 | Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage ]] | | 3 | Yannick | [[ https://www.biorxiv.org/content/10.1101/695338v2.full.pdf | Bifrost - Highly parallel construction and indexing of colored and compacted de Bruijn graphs ]] | | 3 | Marvin | [[ https://www.biorxiv.org/content/10.1101/234856v1.full.pdf | Sequence variation aware genome references and read mapping with the variation graph toolkit ]] | | 4 | Fabian | [[ https://www.liebertpub.com/doi/pdfplus/10.1089/cmb.2019.0309 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment ]] | | 5 | Leonard | [[ https://academic.oup.com/bioinformatics/article/35/19/3599/5372677 | Bit-parallel sequence-to-graph alignment ]] | | | | [[ 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 ]] | | 4 | Aya | [[ https://link.springer.com/content/pdf/10.1186/s13015-020-00164-3.pdf | Alignment- and reference-free phylogenomics with colored de Bruijn graphs ]] | | 5 | Christoph | [[ https://www.biorxiv.org/content/10.1101/645721v1.full.pdf | Viral quasispecies reconstruction via contig abundance estimation in variation graphs ]] | Back to [[:teaching|Teaching]]