hisat2

graph-based alignment of short nucleotide reads to many genomes

Install

All systems
curl cmd.cat/hisat2.sh
Debian Debian
apt-get install hisat2
Ubuntu
apt-get install hisat2
image/svg+xml Kali Linux
apt-get install hisat2
Windows (WSL2)
sudo apt-get update sudo apt-get install hisat2
Dockerfile
dockerfile.run/hisat2

hisat2

graph-based alignment of short nucleotide reads to many genomes

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, 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 the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).