Hi
I am very new to bioinformatics analysis. I am trying to map a whole genome in galaxy, but I don't know exactly how to find my reference genome (chlamydomonas reinhardtii). I do know It is available on NCBI but don't know which file should be used as a reference genome. I mean: is the reference genome only one single file, or is it multiple files for each chromosome? 
I'd be grateful if you could help me.
You can find the representative genome page for your organism at NCBI ([LINK][1]). Actual genome sequence is [in this file][2] which is in fasta format. This is the file you should use as a reference.

If you need specific help with Galaxy then consider posting questions to their help forum: https://help.galaxyproject.org/


  [1]: https://www.ncbi.nlm.nih.gov/genome/147?genome_assembly_id=22881
  [2]: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/595/GCF_000002595.1_v3.0/GCF_000002595.1_v3.0_genomic.fna.gz