Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

[EngyNasr]

Correcting some training explanations in the preprocessing workflow, and adding a missing step in the long version of the training

Thanks @paulzierep for spotting them :)

Thanks,
Engy

[paulzierep]

Thanks Engy. I will go trough it now and add more when I find them:
Next one: Can you explain what samples profile is/means also in the Training:

training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md

Line 163 in 56f7907

> - *"Samples Profile"*: `PacBio/Oxford Nanopore read to reference mapping`

[paulzierep]

Here:

training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.md

Line 299 in 56f7907

In this tutorial, we know the samples come from __chicken__ meat spiked with **_Salmonella_** so we already know what will we get as the host and the main pathogen.

We could add that if the host is not known, kraken2 with calamari could be used to detect it.