====== Computational Pangenomics (2S) ======

| [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=229910028|392230]] | Stoye | Winter 2020/21 | Monday, 10-12 via Zoom |

===== Contents =====

Based on original research papers, the participants will give oral presentations (20-45 min) and write short summaries (ca. 5 pages), both in English, about current algorithmic problems in computational pangenomics and their solutions.

This class will be given as a live video conference. Details will be distributed to registered participants short before the first class on October 26.

===== Schedule =====

^ **Date** ^ **Topic** ^ **Name** ^
| 26.10.2020 | Organisation of the Seminar | Jens S |
| 02.11.2020 | How to talk | Jens S |
| 09.11.2020 | How to write | Jens S |
| 16.11.2020 | -- | -- |
| 23.11.2020 | -- | -- |
| 30.11.2020 | -- | -- |
| 07.12.2020 | -- | -- |
| 14.12.2020 | -- | -- |
| 21.12.2020 | **Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs** G. Holley, P. Melsted. //Genome Biology// **21**, 249 (2020) [[https://doi.org/10.1186/s13059-020-02135-8]] | Yannick P |
| X-mas break |||
| 04.01.2021 | **BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs** N. Luhmann, G. Holley, M. Achtman. //BioRxiv// (2020) [[https://doi.org/10.1101/2020.01.21.914168]] | Ann-Cathrin G |
| 11.01.2021 | **Detecting High Scoring Local Alignments in Pangenome Graphs** T. Schulz, R. Wittler, S. Rahmann, F. Hach, J. Stoye. //BioRxiv// (2020) [[https://doi.org/10.1101/2020.09.03.280958]] | Leonie B |
| 18.01.2021 | **Alignment- and reference-free phylogenomics with colored de Bruijn graphs** R. Wittler. //Algorithms for Molecular Biology// **15**, 4 (2020) [[https://doi.org/10.1186/s13015-020-00164-3]] | Rebecca P |
| 25.01.2021 | **Bit-parallel sequence-to-graph alignment** M. Rautiainen,  V. Mäkinen,  T. Marschall. //Bioinformatics// **35**(19), 3599-3607 (2019) [[https://doi.org/10.1093/bioinformatics/btz162]] | Franziska N |
| 01.02.2021 | **Haplotype threading: accurate polyploid phasing from long reads** S. D. Schrinner, R. Serra Mari, J. Ebler, M. Rautiainen, L. Seillier, J. J. Reimer, B. Usadel, T. Marschall, G. W. Klau. //Genome Biology// **21**, 252 (2020) [[https://doi.org/10.1186/s13059-020-02158-1]] | Ina K |
| 08.02.2021 | -- | -- |

=====Suggested Literature=====

  * **Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage** G. Holley, R. Wittler, J. Stoye. //Algorithms for Molecular Biology// **11**, 3 (2016) [[https://doi.org/10.1186/s13015-016-0066-8]]
  * **Computational pan-genomics: status, promises and challenges** The Computational Pan-Genomics Consortium. //Briefings in Bioinformatics// **19**(1), 118–135 (2018) [[https://doi.org/10.1093/bib/bbw089]]
  * **Variation graph toolkit improves read mapping by representing genetic variation in the reference** E. Garrison, J. Sirén, A. M. Novak, G. Hickey, J. M. Eizenga, E. T. Dawson, W. Jones, S. Garg, C. Markello, M. F Lin, B. Paten, R. Durbin. //Nature Biotechnology// **36**, 875–879 (2018) [[https://doi.org/10.1038/nbt.4227]]
  * **Bit-parallel sequence-to-graph alignment** M. Rautiainen,  V. Mäkinen,  T. Marschall. //Bioinformatics// **35**(19), 3599-3607 (2019) [[https://doi.org/10.1093/bioinformatics/btz162]]
  * **Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph** R. Martiniano, E. Garrison, E. R. Jones, A. Manica, R. Durbin. //Genome Biology// **21**, 250 (2020)  https://doi.org/10.1186/s13059-020-02160-7
  * **Haplotype threading: accurate polyploid phasing from long reads** S. D. Schrinner, R. Serra Mari, J. Ebler, M. Rautiainen, L. Seillier, J. J. Reimer, B. Usadel, T. Marschall, G. W. Klau. //Genome Biology// **21**, 252 (2020) [[https://doi.org/10.1186/s13059-020-02158-1]]
  * **GraphAligner: rapid and versatile sequence-to-graph alignment** M. Rautiainen, T. Marschall. //Genome Biology// **21**, 253 (2020) [[https://doi.org/10.1186/s13059-020-02157-2]]
  * **Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs** G. Holley, P. Melsted. //Genome Biology// **21**, 249 (2020) [[https://doi.org/10.1186/s13059-020-02135-8]]
  * **Efficient Construction of a Complete Index for Pan-Genomics Read Alignment** A. Kuhnle, T. Mun, C. Boucher, T. Gagie, B. Langmead, G. Manzini. //Journal of Computational Biology// **27**(4), 500-513 (2020) [[https://doi.org/10.1089/cmb.2019.0309]]
  * **Alignment- and reference-free phylogenomics with colored de Bruijn graphs** R. Wittler. //Algorithms for Molecular Biology// **15**, 4 (2020) [[https://doi.org/10.1186/s13015-020-00164-3]]
  * **Strain-aware assembly of genomes from mixed samples using flow variation graphs** J. A. Baaijens, L. Stougie,  A. Schönhuth. //BioRxiv// (2020) [[https://doi.org/10.1101/645721]]
  * **BlastFrost: Fast querying of 100,000s of bacterial genomes in Bifrost graphs** N. Luhmann, G. Holley, M. Achtman. //BioRxiv// (2020) [[https://doi.org/10.1101/2020.01.21.914168]]
  * **Detecting High Scoring Local Alignments in Pangenome Graphs** T. Schulz, R. Wittler, S. Rahmann, F. Hach, J. Stoye. //BioRxiv// (2020) [[https://doi.org/10.1101/2020.09.03.280958]]