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.