Source: hisat2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
               help2man,
               pandoc,
               python3
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/hisat2
Vcs-Git: https://salsa.debian.org/med-team/hisat2.git
Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml

Package: hisat2
Architecture: any
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${perl:Depends},
         python3
Recommends: python3-hisat2,
            bcftools,
            samtools
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).

# Package: python3-hisat2
# Section: python
# Architecture: all
# Depends: ${misc:Depends},
#          hisat2,
#          python3
# Description: Python scripts accompanying hisat2
#  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).
#  .
#  This package provides a serires of platform-independent scripts that are
#  typically expected to be co-installed with the hisat2 binary.
