Salmon: indexing genome and transcriptome

With salmon 1.0.0+ we should prepare and index genome+transcriptome in the following manner:
https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/

Please take a look here: https://www.biorxiv.org/content/10.1101/138800v2
Authors also emphasize this on salmon gitter channel.

Edit:

That is also what they recommend in the docs (section 3.2):
https://readthedocs.org/projects/salmon/downloads/pdf/latest/