I work on mitochondrial genome of Bivalvia. I would like to align reads generated by NGS platform Illumina. I would like use "Map with Bowtie for Illumina" but no reference genome corresponds to my data. Is it possible to add the mitochondrial genome of Arctica islandica : http://www.ncbi.nlm.nih.gov/nuccore/NC_022709.1 ; and the mitochondrial genome of Venerupis philippinarum : http://www.ncbi.nlm.nih.gov/nuccore/NC_003354.1 on Galaxy?
Thank you for your help.