21 months ago by
Yes, for the BWA tools wrapped for Galaxy, the forward and reverse reads are expected to be in distinct datasets and entered that way on the tool form.
Concatenate means to place one file on top of the other (stack the content). This would create a single dataset that would probably run through the tool, but the results would not be optimal (permit the informational use of the paired-end mapping placements).
If you mean instead that the sequences will be either joined end-to-end or assembled (when there is overlap), there are use cases for that but I don't think it is part of the cloudmap workflow/excepted inputs. However, if you have questions about these tools/workflows, the authors take questions - see the links near the bottom of the tool forms.
More about the types of NGS reads in detail to better understand the content: https://wiki.galaxyproject.org/Learn/GalaxyNGS101#Overview_of_NGS_technologies
Thanks, Jen, Galaxy team