Introduction

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). Based on an extension of BWT for a graph, a graph FM index (GFM) has been designed and implemented. 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).

For more information, visit the official HISAT2 website.

Programming language: C++

Brief description: fast and sensitive alignment program.

Open source license: GPL 3.0