Package: hisat2 (2.2.1-5~0exp) [debports]

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Experimental package

Warning: This package is from the experimental distribution. That means it is likely unstable or buggy, and it may even cause data loss. Please be sure to consult the changelog and other possible documentation before using it.

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).

Other Packages Related to hisat2

• dep: libc6 (>= 2.34) [riscv64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

• dep: libc6.1 (>= 2.36) [ia64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6.1-udeb

• dep: libgcc-s1 (>= 3.4) [riscv64]

  GCC support library

  dep: libgcc-s1 (>= 4.2) [ia64]

• dep: libstdc++6 (>= 11)

  GNU Standard C++ Library v3

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• rec: bcftools

  genomic variant calling and manipulation of VCF/BCF files

• rec: python3-hisat2

  Python scripts accompanying hisat2

• rec: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

Download hisat2

Download for all available architectures

Architecture	Package Size	Installed Size	Files
ia64 (unofficial port)	4,648.6 kB	20,828.0 kB	[list of files]
riscv64 (unofficial port)	3,751.1 kB	12,691.0 kB	[list of files]