i am using bowtie 2 and i didn’t find my reference genome Caenorhabditis elegans ce11.
That reference genome is indexed at UseGalaxy.eu for
Bowtie2. Please try there.
You can have one account at each of the public Galaxy servers. Each account/server will have different resources: account quota allocation, tools and indexes hosted, computational resources.
How to move data between servers: Transfer entire histories from one Galaxy server to another