Are there any tools in Galaxy to align short reads against multiple reference
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! :)
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