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Computational Pangenomics (2S)

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