Manual For Wrapper - -x The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.-1 . A not always very easy to read, but practical copy & paste format has been chosen throughout this manual. In this format all commands are represented in code boxes, where the comments are given in blue color.To save space, often several commands are concatenated on.