Hisat2-Build
Where: Run hisat2-build in the
same folder as your genome. (Use File --> OpenDir to open a new
window in your genome folder.)
What:
Base name for index files - hisat2-build will create a number
of files with the .ht2 extension. The names for all of these files
will begin with the same string. If the genome file was
GCF_000005005.2_B73_RefGen_v4_genomic.fna, a short name to paste
into this field might be B73_RefGen_v4. Output files would then be
B73_RefGen_v4.ht1, B73_RefGen_v4.ht2 etc.