General introduction about the topic and then an introduction of the tutorial (the questions and the objectives). It is nice also to have a scheme to sum up the pipeline used during the tutorial. The idea is to give to trainees insight into the content of the tutorial and the (theoretical and technical) key concepts they will learn.

You may want to cite some publications; this can be done by adding citations to the bibliography file (tutorial.bib file next to your tutorial.md file). These citations must be in bibtex format. If you have the DOI for the paper you wish to cite, you can get the corresponding bibtex entry using doi2bib.org.

With the example you will find in the tutorial.bib file, you can add a citation to this article here in your tutorial like this: {% cite Batut2018 %}. This will be rendered like this: Batut et al. 2018, and links to a bibliography section which will automatically be created at the end of the tutorial.

Please follow our tutorial to learn how to fill the Markdown

Agenda

In this tutorial, we will cover:

1. Galaxy and data preparation
2. Pangenomics
3. Multi-sequence alignment
4. Conclusion

Galaxy and data preparation

Hands On: Data Upload

1. Create a new history for this analysis

   Tip: Creating a new history

   To create a new history simply click the new-history icon at the top of the history panel:

   

2. Rename the history

   Tip: Renaming a history

   1. Click on galaxy-pencil (Edit) next to the history name (which by default is “Unnamed history”)
   2. Type the new name
   3. Click on Save
   4. To cancel renaming, click the galaxy-undo “Cancel” button

   If you do not have the galaxy-pencil (Edit) next to the history name (which can be the case if you are using an older version of Galaxy) do the following:

   1. Click on Unnamed history (or the current name of the history) (Click to rename history) at the top of your history panel
   2. Type the new name
   3. Press Enter

3. Import the contig file from Zenodo or from Galaxy shared data libraries:

   https://zenodo.org/records/1/files/DRR187559_contigs.fasta
   

   Tip: Importing via links

   • Copy the link location

   • Click galaxy-upload Upload Data at the top of the tool panel

   • Select galaxy-wf-edit Paste/Fetch Data

   • Paste the link(s) into the text field

   • Press Start

   • Close the window

   Tip: Importing data from a data library

   As an alternative to uploading the data from a URL or your computer, the files may also have been made available from a shared data library:

   1. Go into Libraries (left panel)
   2. Navigate to the correct folder as indicated by your instructor.
      • On most Galaxies tutorial data will be provided in a folder named GTN - Material –> Topic Name -> Tutorial Name.
   3. Select the desired files
   4. Click on Add to History galaxy-dropdown near the top and select as Datasets from the dropdown menu

   5. In the pop-up window, choose

      • “Select history”: the history you want to import the data to (or create a new one)
   6. Click on Import

Pangenomics

Hands On: Task description

1. PPanGGOLiN all ( Galaxy version 2.2.1+galaxy1) with the following parameters:
   • param-collection “Select genome files”: Input dataset collection

TODO: Consider adding a question to test the learners understanding of the previous exercise

Question

1. Question1?
2. Question2?

Solution

1. Answer for question1
2. Answer for question2

Multi-sequence alignment

Hands On: Task description

1. PPanGGOLiN MSA ( Galaxy version 2.2.1+galaxy1) with the following parameters:
   • param-file “Input pangenome h5 file”: pangenome_h5 (output of PPanGGOLiN all tool)
   • “Partition”: Core

TODO: Consider adding a question to test the learners understanding of the previous exercise

Question

1. Question1?
2. Question2?

Solution

1. Answer for question1
2. Answer for question2

Conclusion

Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the pipeline used.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• to do

• to do

Frequently Asked Questions

• Topic FAQs
• Galaxy FAQs
• GTN Matrix Chat
• Galaxy Help Forum

References

1. Batut, B., S. Hiltemann, A. Bagnacani, D. Baker, V. Bhardwaj et al., 2018 Community-Driven Data Analysis Training for Biology. Cell Systems 6: 752–758.e1. 10.1016/j.cels.2018.05.012

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Citing this Tutorial

1. Guillaume Gautreau, Hélène Chiapello, Bérénice Batut, Valentin Loux, Bacterial pangenomics (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{genome-annotation-bacterial-pangenomics,
author = "Guillaume Gautreau and Hélène Chiapello and Bérénice Batut and Valentin Loux",
	title = "Bacterial pangenomics (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/genome-annotation/tutorials/bacterial-pangenomics/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools:
- name: ppanggolin_all
  owner: iuc
  revisions: a83148dac159
  tool_panel_section_label: Annotation
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: ppanggolin_msa
  owner: iuc
  revisions: 76170454dc91
  tool_panel_section_label: Annotation
  tool_shed_url: https://toolshed.g2.bx.psu.edu/

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