Bug#834592: ITP: hisat2 -- graph-based alignment of short nucleotide reads to many genomes

["Michael R. Crusoe" <michael.crusoe@gmail.com>]

Package: wnpp
Severity: wishlist
Owner: Debian Med team <debian-med@lists.debian.org>

* Package name    : hisat2
  Version         : 2.0.4
  Upstream Author : HISAT2 team <hisat2.genomics@gmail.com>
* URL             : https://ccb.jhu.edu/software/hisat2/index.shtml
* License         : GPL-3+
  Programming Lang: Perl, Python, C++
  Description     : 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).

hisat2 will be team-maintained by the Debian Med team.