Welcome, @Shailesh_Kumar_Dhuda
You can map against any reference genome in Galaxy. You’ll need to source the fasta, load it into a Galaxy history, then choose the “from the history” option on the tool form.
Please start here → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj
For loading the reference genome fasta, you can usually just copy/paste the file URL from a public source into the Upload tool. Or, locally browse and file on your computer and load the file that way.
Then, for mapping in general, please see the tutorials here to start with.
- Using a reference genome index already on the server → Hands-on: Mapping / Mapping / Sequence analysis
- Using a reference genome fasta from the history → Hands-on: SARS-CoV-2 Viral Sample Alignment and Variant Visualization / SARS-CoV-2 Viral Sample Alignment and Variant Visualization / Sequence analysis
If you haven’t used Galaxy before, we have some simple “first time” tutorials here, too.
If I misunderstood what you are trying to do, or you need detailed help, please explain a bit more please. 