Add new tutorial for deciphering viral populations using SNV and baculovirus isolates (Variant analysis)

[wennj]

Dear GTN Team,

I am a new contributor and have created a tutorial for analysing virus populations using SNV (and using the example of large dsDNA viruses). The workflow is based on published results and follows a scientific approach. I have followed the GTN instructions as closely as possible (and as I understand them). Please excuse any mistakes in using Github. The tutorial has also been reviewed by a student.

Key changes:

• Added a new step-by-step tutorial (variant-analysis/baculovirus-isolate-variation) for analysing viral populations on the example of baculovirus isolates
• CONTRIBUTORS.yaml was changed.

Checked:

• Images can be re-hosted.

Help:

• One image in the introduction is linked to ICTV.global. Allowed?

TODO:

• Tool bcftools mpileup / bcftools call are using DPR (deprecated but functional). Needs to be changed to AD in the future.
• Awaiting feedback and suggestions for improvement.
• Refine the tutorial based on reviewer comments.

Best,
JTW

[bgruening]

Very cool! Welcome @wennj!

I have added a few batch of comments, if you agree with them you can accept them from inside the github interface.

[wennj]

@bgruening Many thanks for the suggestions and feedback. I have addressed all comments. As this is my first tutorial and my first pull request, I hope everything is checked correctly.

[bgruening]

Thanks a lot! Let's wait for some experts in this area to get some content feedback.

Can you please add the jki to this file as well: https://github.com/galaxyproject/training-material/blob/main/ORGANISATIONS.yaml this will then generate a page like: https://training.galaxyproject.org/hall-of-fame/uni-freiburg/

[wennj]

Thanks a lot! Let's wait for some experts in this area to get some content feedback.

Can you please add the jki to this file as well: https://github.com/galaxyproject/training-material/blob/main/ORGANISATIONS.yaml this will then generate a page like: https://training.galaxyproject.org/hall-of-fame/uni-freiburg/

I would like to check that first with my administration. Can this also be done at a later stage?

[wm75]

Very nice work @wennj !
Those awk expressions are rather intimidating for beginners I guess, but also elegant compared to multi-step solutions with other tools.
Can be interesting to teach them :-)

[wm75]

Suggested change

	> - {% icon param-collection %} *"Select a paired collection"*: `output` (output of **Download and Extract Reads in FASTAQ format from NCBI SRA** {% icon tool %})
	> - {% icon param-collection %} *"Select a paired collection"*: `Paired-end data (fastq-dump)` (output of **Download and Extract Reads in FASTAQ format from NCBI SRA** {% icon tool %})

In general, in the GTN we are not using a tool's output name (as defined in the tool wrapper), but the user facing label of the generated dataset if that is a nice one, or a label-like description of the dataset. Take a look at https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb_transmission/tutorial.html as an example, then change most of your hands-on boxes accordingly.

[wm75]

Can you improve the wording of this question? It's not easy to understand.

[wm75]

You are mostly talking about isolates, but sometimes also about populations or samples.
I realize the terminology around the concept may be the source of endless debates, but maybe you could reserve a small paragraph in the introduction for explaining what an isolate is in the context here and why it can be a mix of things.