HISAT2 is a fast and highly sensitive next-generation sequencing read alignment tool, suitable for alignment analysis of whole genome, transcriptome and exonome sequencing data. Its core technology is the Graph FM index (GFM), which enables sequencing reads to be aligned to a population reference genome that includes common genetic variations, rather than a single reference genome. HISAT2 adopts the hierarchical Graph FM index (HGFM) architecture, covering the entire genome through a large number of local small indexes, effectively improving the alignment speed and accuracy. This tool performs particularly well in SNP read alignment, with an approximate memory usage of 6.7 GB.