We are trying to put a few reference genomes into the built-in index for bwa, 
bowtie, bowtie2 and tophat.  For the human hg19 we can find those.  However, we 
also like to upload the Rhesus macaque genome and haven't been able to find an 
indexed version at NCBI or other places.

Are other genomes pre-indexed for these applications somewhere?
How do those files look like exactly (extensions, number of files needed, etc.)?
How would we index the Rhesus genome for the above mappers if they are not 
available in an indexed form?

Thank you,

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