I am looking to use the latest of the sus scrofa genome in HISAT2 for BAM alignment.
How to use the genome?
Welcome, @KMasu
It seems that the most current assembly would be:
Feb. 2017 (SGSC Sscrofa11.1/susScr11)
XRef: UCSC Genome Browser Downloads #pig
We can probably add that genome as a native index for tools at the UseGalaxy public servers but it will not be immediate. Don’t wait for this.
For immediate use, you can load up the reference genome fasta and use it as a custom reference genome. Consider getting the reference annotation at the same time and from the same data provider (UCSC).
How to → FAQ: How to use Custom Reference Genomes?
Update: If you work at UseGalaxy.eu, this exact genome index is already available. At the other servers, not yet. You will still need to pull in the reference annotation if you plan to use that sort of data. Get it from UCSC the same as you would any genome (native or custom).