Package: bowtie2 (2.5.3-1 and others)

[ Source: bowtie2  ]

ultrafast memory-efficient short read aligner

is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

Tags: Biology: Nucleic Acids, Field: Biology, field::biology:bioinformatics, implemented-in::c++, User Interface: Command Line, Role: role::program, use::comparing, Works with: Biological Sequence

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• dep: libc6 (>= 2.29) [m68k]

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

  dep: libc6 (>= 2.31) [sh4]

  dep: libc6 (>= 2.33) [ppc64, sparc64]

  dep: libc6 (>= 2.34) [amd64, arm64, mips64el, ppc64el, riscv64]

• dep: libc6.1 (>= 2.29) [alpha]

  GNU C Library: Shared libraries
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  dep: libc6.1 (>= 2.37) [ia64]

• dep: libgcc-s1 (>= 3.0) [not alpha, amd64, ia64, m68k, sh4]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [amd64]

  dep: libgcc-s1 (>= 4.2) [ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC support library

• dep: libgcc1 (>= 1:3.4) [alpha]

  Package not available

• dep: libstdc++6 (>= 11) [ppc64, sparc64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [not alpha, m68k, ppc64, sh4, sparc64]

  dep: libstdc++6 (>= 9) [alpha, m68k, sh4]

• dep: libunwind8 [ia64]

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• dep: perl

  Larry Wall's Practical Extraction and Report Language

• dep: python3

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

• dep: zlib1g (>= 1:1.2.6)

  compression library - runtime

• sug: bowtie2-examples

  Examples for bowtie2

Download bowtie2

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	2.3.5.1-6	1,666.9 kB	6,178.0 kB	[list of files]
amd64	2.5.3-1	1,404.0 kB	5,684.0 kB	[list of files]
arm64	2.5.3-1	1,308.1 kB	5,062.0 kB	[list of files]
ia64 (unofficial port)	2.5.1-1	2,341.5 kB	11,597.0 kB	[list of files]
m68k (unofficial port)	2.4.2-2+b1	1,202.1 kB	5,463.0 kB	[list of files]
mips64el	2.5.3-1	1,389.0 kB	6,186.0 kB	[list of files]
ppc64 (unofficial port)	2.4.5-1	1,346.4 kB	5,825.0 kB	[list of files]
ppc64el	2.5.3-1	1,454.9 kB	5,960.0 kB	[list of files]
riscv64	2.5.3-1	1,597.8 kB	4,664.0 kB	[list of files]
sh4 (unofficial port)	2.4.2-2+b1	1,683.6 kB	4,651.0 kB	[list of files]
sparc64 (unofficial port)	2.4.5-1	1,197.3 kB	5,155.0 kB	[list of files]