Introduction

Agenda

In this tutorial, we will cover:

1. Get genomes from GTDB
2. Extract IDs for NCBI
3. Download genomes from NCBI
4. Conclusion

Get genomes from GTDB

Hands On: Task description

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

Extract IDs for NCBI

Hands On: Task description

1. Cut with the following parameters:
   • “Cut columns”: c1
   • “Delimited by”: Comma
   • param-file “From”: output (Input dataset)

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

Hands On: Task description

1. Cut with the following parameters:
   • “Cut columns”: c6
   • param-file “From”: output (Input dataset)

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

Hands On: Task description

1. Concatenate datasets with the following parameters:
   • param-file “Concatenate Dataset”: out_file1 (output of Cut tool)
   • In “Dataset”:
     • param-repeat “Insert Dataset”
       • param-file “Select”: out_file1 (output of Cut tool)

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

Hands On: Task description

1. Sort with the following parameters:
   • param-file “Sort Dataset”: out_file1 (output of Concatenate datasets tool)
   • “on column”: c1
2. Unique ( Galaxy version 0.3) with the following parameters:
   • param-file “from query”: out_file1 (output of Sort tool)
   • “Advanced Options”: Hide Advanced Options

   TODO: Check parameter descriptions

   TODO: Consider adding a comment or tip box

   Comment: short description

   A comment about the tool or something else. This box can also be in the main text

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

Hands On: Task description

1. Remove beginning with the following parameters:
   • “Remove first”: 2
   • param-file “from”: outfile (output of Unique tool)

   TODO: Check parameter descriptions

   TODO: Consider adding a comment or tip box

   Comment: short description

   A comment about the tool or something else. This box can also be in the main text

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

Download genomes from NCBI

Hands On: Task description

1. NCBI Datasets Genomes ( Galaxy version 16.42.0+galaxy0) with the following parameters:
   • In “Query”:
     • “Choose how to find genomes to download”: By NCBI assembly or BioProject accession
       • “Enter accession or read from file ?”: Read a list of NCBI Assembly accessions from a dataset
         • param-file “Select dataset with list of NCBI Assembly accessions”: out_file1 (output of Remove beginning tool)

   TODO: Check parameter descriptions

   TODO: Consider adding a comment or tip box

   Comment: short description

   A comment about the tool or something else. This box can also be in the main text

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

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Citing this Tutorial

1. Hélène Chiapello, Bérénice Batut, Valentin Loux, Dataset construction for bacterial comparative genomics (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/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-comparative-genomics-dataset-construction,
author = "Hélène Chiapello and Bérénice Batut and Valentin Loux",
	title = "Dataset construction for bacterial comparative genomics (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/bacterial-comparative-genomics-dataset-construction/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-comparative-genomics-dataset-construction/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: unique
  owner: bgruening
  revisions: 7ce75adb93be
  tool_panel_section_label: Text Manipulation
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
- name: ncbi_datasets
  owner: iuc
  revisions: d951c5b0edd1
  tool_panel_section_label: Get Data
  tool_shed_url: https://toolshed.g2.bx.psu.edu/

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