Computational Pangenomics (2S)

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.

• 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