Introduction

HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. It includes a new indexing scheme based on the Burrows-Wheeler transform (BWT) and the FM index, called hierarchical indexing, that employs the two types of indexes: one global FM index representing the whole genome, and many separate local FM indexes for small regions collectively covering the genome. All these together, HISAT enables extremely fast and sensitive alignment of reads, in particular those spanning two exons or more.

For more information, visit the official HISAT website.

Programming language: C/C++

Brief description: a fast and sensitive spliced alignment program for mapping RNA-seq reads

Open source license: GPL