Hi, 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, Jeannette CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.