Are there any tools in Galaxy to align short reads against multiple reference 
sequences?

I have a dozen microbial genomes sequenced for which there are 2 reference 
genomes already sequenced. We have tried aligning each of these individually 
against either of the reference genomes - some align better against the first 
reference genome, some align better against the second reference genome. 
Ideally though I would like to be able to align against both at the same time. 
Is this possible?

I have found a tool called GenomeMapper and hints of 2 other tools in 
development that do something like this, but nothing for Galaxy yet.

How do others proceed with this type of problem? Workflows appreciated! :)

 -John

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