Hi Vijay, For right now, using a Custom reference genome with these tools is the best solution: http://wiki.galaxyproject.org/Support#Custom_reference_genome This genome in Galaxy is sourced from UCSC, as you probably know: http://wiki.galaxyproject.org/Support#Reference_genomes The longer-term strategy for new/updated indexes will be worked out soon. Our immediate goal was to get the tools out on Main as soon as possible. Thanks, Jen Galaxy team On 8/13/13 1:20 PM, Vijay Kumar wrote:

Dear sir, please add reference genome of Zebra finch genome in Bowtie2 and Tophat2 option in galaxy. thank u

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