HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for a graph , we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover human population). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of sequencing reads. This new indexing scheme is called Hierarchical Graph FM index (HGFM). We have developed HISAT2 based on the HISAT  and Bowtie 2  implementations. See the HISAT2 website for more information.
HISAT2 requires a 64-bit computer running either Linux or Mac OS X and at least 8 GB of RAM.
A few notes:
git clone https://github.com/DaehwanKimLab/hisat2.git cd hisat2 make
hisat2-build builds a HISAT2 index from a set of DNA sequences.
hisat2-build outputs a set of 6 files with
In the case of a large index these suffixes will have a
These files together constitute the index: they are all that is needed to align reads to that reference.
The original sequence FASTA files are no longer used by HISAT2 once the index is built.
Example for HISAT2 index building:
hisat2-build genome.fa genome
Examples alignment with HISAT2:
# for single-end FASTA reads DNA alignment hisat2 -f -x genome -U reads.fa -S output.sam --no-spliced-alignment # for paired-end FASTQ reads alignment hisat2 -x genome -1 reads_1.fq -2 read2_2.fq -S output.sam
 Sirén J, Välimäki N, Mäkinen V (2014) Indexing graphs for path queries with applications in genome research. IEEE/ACM Transactions on Computational Biology and Bioinformatics 11: 375–388. doi: 10.1109/tcbb.2013.2297101
 Kim D, Langmead B, and Salzberg SL HISAT: a fast spliced aligner with low memory requirements, Nature methods, 2015
 Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9:357-359
Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019)
Zhang, Y., Park, C., Bennett, C., Thornton, M. and Kim, D Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N Genome Research 31(7): 1290-1295 (2021)