Yes. Bowtie and BWA mappers will align illumina reads against a
reference genome. Take a look at our quickie #7 at http://usegalaxy.org
On Jan 15, 2010, at 3:11 PM, Michaela Lee wrote:
I was wondering if Galaxy can align Solexa reads to a reference
sequence. If not, can I upload my alignment data from Maq onto
Galaxy and somehow work with that data online? Also, can Galaxy
tell me which parts of the reference sequence have no reads aligned
to them? I am basically trying to figure out which parts were not
sequenced and compare those sequences between different subjects.
Thanks for your help.
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