Creating a Bowtie2 Index for S.Purpuratus to use in Galaxy

Question

[alice_pieplow]

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!

Answer 1

[GenoMax]

Download the genome in fasta format from here. Upload to galaxy and then create bowtie2 index.

[Friederike]

Just adding to what genomax wrote: Upload the FASTA file of the genome into your history and then you will be able to choose "Use a genome from the history and build index" when asked about the reference during the alignment step.

[alice_pieplow]

It worked perfectly! Thanks so much :)