I want to index the hg19.fa for hisat2 usage, I know that the generic command line is
hisat2-build [options]* <reference_in> <ht2_base>
I m slowly getting familiar with commands but now I wanted to ask you what should I use in the [options] ? in the manual there are severals but I don’t know which one is the right to use in this case/
Can be ok this one?
Hisa2-build hg19.fa hg19-indexed
Where hg19-indexed is my output
Or, Is there a website where I can download an indexed and ready to use ?