Package: hisat2 (2.2.1-5 and others)

[ Source: 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).

Other Packages Related to hisat2

• dep: libc6 (>= 2.29) [x32]

  GNU C könyvtár: megosztott könyvtárak
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.38) [not alpha, ia64, x32]

• dep: libc6.1 (>= 2.34) [alpha]

  GNU C könyvtár: megosztott könyvtárak
  also a virtual package provided by libc6.1-udeb

  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, mips64el, ppc64, ppc64el, s390x, x32]

  GCC támogató programkönyvtár

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sparc64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386, ia64]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC támogató programkönyvtár

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC támogató programkönyvtár

• dep: libstdc++6 (>= 13.1) [not x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 9) [x32]

• 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	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.2.1-5	3,723.9 kB	14,324.0 kB	[list of files]
amd64	2.2.1-5+b1	3,716.7 kB	14,675.0 kB	[list of files]
arm64	2.2.1-5+b2	3,493.3 kB	13,419.0 kB	[list of files]
armel	2.2.1-5+b1	3,465.4 kB	13,653.0 kB	[list of files]
armhf	2.2.1-5+b1	3,412.6 kB	12,055.0 kB	[list of files]
hppa (unofficial port)	2.2.1-5	3,910.1 kB	14,542.0 kB	[list of files]
i386	2.2.1-5+b1	3,629.3 kB	15,219.0 kB	[list of files]
ia64 (unofficial port)	2.2.1-4+b3	4,617.6 kB	20,576.0 kB	[list of files]
m68k (unofficial port)	2.2.1-5+b1	3,452.0 kB	14,573.0 kB	[list of files]
mips64el	2.2.1-5+b1	3,543.7 kB	14,549.0 kB	[list of files]
ppc64 (unofficial port)	2.2.1-5+b1	3,588.0 kB	14,251.0 kB	[list of files]
ppc64el	2.2.1-5+b1	3,652.9 kB	14,187.0 kB	[list of files]
riscv64	2.2.1-5+b1	3,821.9 kB	12,775.0 kB	[list of files]
s390x	2.2.1-5+b1	3,246.2 kB	13,693.0 kB	[list of files]
sparc64 (unofficial port)	2.2.1-5+b1	3,383.5 kB	15,875.0 kB	[list of files]
x32 (unofficial port)	2.2.0-2	3,563.7 kB	14,217.0 kB	[list of files]