I want to align some WGS data I have for S. purpruatus (purple urchin) using bowtie2 in Galaxy, but the reference genome for the organism is not available. I have the option to upload my own reference index- how do I make one? I believe this is the most current reference genome; where do i start? ftp://ftp.ncbi.nih.gov/genomes/Strongylocentrotus_purpuratus/
I am honestly so new to this- I dont even know which of these file directories contains the actual genome, it looks like a lot of them are transcripts or annotations. Any help is greatly appreciated!