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joannmudge committed Feb 6, 2025
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46 changes: 35 additions & 11 deletions module_notebooks/01-intro-to-pangenomics.ipynb
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"\n",
"+ Sigaux F. Génome du cancer ou de la construction des cartes d'identité moléculaire des tumeurs [Cancer genome or the development of molecular portraits of tumors]. Bull Acad Natl Med. 2000;184(7):1441-7; discussion 1448-9. French. PMID: 11261250.\n",
"\n",
"![Sigaux et al.](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Abstract1.png)\n",
"![Sigaux et al.](./Figures/Abstract1.png)\n",
"\n",
"The term was later revitalized by Tettelin et al. to describe a microbial genome by which genes were in the core (present in all strains) and which genes were dispensable (missing from one or more of the strains).\n",
"\n",
"![Tettelin et al.](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Abstract2.png)\n",
"![Tettelin et al.](./Figures/Abstract2.png)\n",
"\n",
"+ Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., ... & Fraser, C. M. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences, 102(39), 13950-13955.\n",
"\n",
"![Pangenome: https://en.wikipedia.org/wiki/Pan-genome](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Pangenome.png)\n",
"![Pangenome: https://en.wikipedia.org/wiki/Pan-genome](./Figures/Pangenome.png)\n",
"\n",
"#### Open vs. Closed Genomes\n",
"\n",
"![Open and Closed Pangenomes: https://en.wikipedia.org/wiki/Pan-genome](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/ClosedvOpen.png)\n",
"![Open and Closed Pangenomes: https://en.wikipedia.org/wiki/Pan-genome](./Figures/ClosedvOpen.png)\n",
"\n",
"#### Then vs. Now\n",
"\n",
"![Cost per Genome: https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/CostGenome.png)\n",
"![Cost per Genome: https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data](./Figures/CostGenome.png)\n",
"\n",
"- Low Cost\n",
"- High Quality Long Reads (HiFi)\n",
"- Many reference-quality assemblies per species\n",
"\n",
"![Pangenome Publications: https://www.nature.com/articles/s41477-020-0733-0](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/GenomePubs.png)\n",
"![Pangenome Publications: https://www.nature.com/articles/s41477-020-0733-0](./Figures/GenomePubs.png)\n",
"\n",
"#### \"Pangenome\" Today\n",
"\n",
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"\n",
"“Questions about efficient data structures, algorithms and statistical methods to perform bioinformatic analyses of pan-genomes give rise to the discipline of ‘computational pan-genomics’.”\n",
"\n",
" ![Computational Pangenomics: https://academic.oup.com/bib/article/19/1/118/2566735](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Computational.png) \n",
" ![Computational Pangenomics: https://academic.oup.com/bib/article/19/1/118/2566735](./Figures/Computational.png) \n",
"\n",
"#### Pangenome Representations\n",
"\n",
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"+ Graphs can be acyclic or cyclic\n",
"+ Haplotypes are “threaded” through graph as paths\n",
"\n",
"![Pangenome Representations: https://academic.oup.com/bib/article/19/1/118/2566735](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/VariationGraphA.png)\n",
"![Pangenome Representations: https://academic.oup.com/bib/article/19/1/118/2566735](./Figures/VariationGraphA.png)\n",
"\n",
"![Pangenome Representations: https://academic.oup.com/bib/article/19/1/118/2566735](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/VariationGraphB.png)\n",
"![Pangenome Representations: https://academic.oup.com/bib/article/19/1/118/2566735](./Figures/VariationGraphB.png)\n",
"\n",
"#### Types of Variation Graphs\n",
"\n",
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"\n",
"#### Mapping Reads to Variation Graphs\n",
"\n",
"![Genotyping Variation: https://link.springer.com/article/10.1186/s13059-020-1941-7](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/ReadsToVariation.png)\n",
"![Genotyping Variation: https://link.springer.com/article/10.1186/s13059-020-1941-7](./Figures/ReadsToVariation.png)\n",
"\n",
"### Pangenome Data Sets\n",
"\n",
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34 changes: 29 additions & 5 deletions module_notebooks/02-building-graphs-with-pggb.ipynb
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"\n",
"Critically, pggb performs graph *normalization* to ensure that paths through the graph (e.g. chromosomes) have a linear structure while allowing for cyclic graph structures that capture structural variation.\n",
"\n",
"![Input Genomes](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/pggbFlowDiagram.png)\n",
"![Input Genomes](./Figures/pggbFlowDiagram.png)\n",
"\n",
"### Reference-Free Graphs\n",
"\n",
"https://academic.oup.com/bioinformatics/article/30/24/3476/2422268\n",
"\n",
"![Input Genomes](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/InputGenomes.png)\n",
"![Input Genomes](./Figures/InputGenomes.png)\n",
"\n",
"### PGGB Algorithm\n",
"\n",
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" + 7 Saccharomyces cerevisiae (brewer’s yeast), including the S288C reference\n",
" + 5 *Saccharomyces paradoxus* (wild yeast)\n",
"\n",
"![Yeast Genomes: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Yeast.png)\n",
"![Yeast Genomes: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/](./Figures/Yeast.png)\n",
"\n",
"Yeast genomes are ~12 Mb and have 16 chromosomes.\n",
"\n",
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"\n",
"We will use SK1 reads later on to call variants\n",
"\n",
"![Yeast Genomes: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/YeastB.png)\n",
"![Yeast Genomes: https://yjx1217.github.io/Yeast_PacBio_2016/welcome/](./Figures/YeastB.png)\n",
"\n"
]
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32 changes: 28 additions & 4 deletions module_notebooks/03-indexing-graphs-with-vg.ipynb
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"\n",
"Citation:\n",
"\n",
"![Garrison, E., Sirén, J., Novak, A. et al.](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/VGref.png)\n",
"![Garrison, E., Sirén, J., Novak, A. et al.](./Figures/VGref.png)\n",
"\n",
"![vg Graph Genomics Pipeline: https://github.com/vgteam/vg](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/VGpipe.png)\n",
"![vg Graph Genomics Pipeline: https://github.com/vgteam/vg](./Figures/VGpipe.png)\n",
"\n",
"\n",
"A reference genome \"decorated\" with variants:\n",
"\n",
"![GRAF™ Pan Genome Reference: https://www.sevenbridges.com/graf/](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/GRAF.png)\n",
"![GRAF™ Pan Genome Reference: https://www.sevenbridges.com/graf/](./Figures/GRAF.png)\n",
" "
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30 changes: 27 additions & 3 deletions module_notebooks/07-visualization.ipynb
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"\n",
"Pangenomic graphs can be very complex, often looking like \"hairballs\". Bandage allows us to zoom in on interesting regions to visualize and interact with them.\n",
"\n",
"![Compressed de Bruijn graphs “hairballs”: https://academic.oup.com/bioinformatics/article/30/24/3476/2422268](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/hairballsB.png)\n"
"![Compressed de Bruijn graphs “hairballs”: https://academic.oup.com/bioinformatics/article/30/24/3476/2422268](./Figures/hairballsB.png)\n"
]
},
{
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"Bandage is an interactive graph visualizer. The Bandage acronym stands for:\n",
"a **B**ioinformatics **A**pplication for **N**avigating **D**e novo **A**ssembly **G**raphs **E**asily\n",
"\n",
"![Bandage: https://rrwick.github.io/Bandage/](/home/jupyter/NIGMS-Sandbox-Pangenomics-Module/module_notebooks/Figures/Bandage.png)\n",
"![Bandage: https://rrwick.github.io/Bandage/](./Figures/Bandage.png)\n",
"\n",
"In addition to visualizing graphs, Bandage has BLAST integration that allows you to query the graph with DNA sequences.\n",
"\n",
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