Package: bowtie (1.3.1-3 and others)

[ Source: bowtie  ]

Ultrafast memory-efficient short read aligner

This package addresses the problem to interpret the results from the latest (2010) DNA sequencing technologies. Those will yield fairly short stretches and those cannot be interpreted directly. It is the challenge for tools like Bowtie to give a chromosomal location to the short stretches of DNA sequenced per run.

Bowtie aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::c++, interface::commandline, Role: Program, Science: science::calculation, scope::utility, Purpose: Analysing, use::comparing, works-with::biological-sequence

Other Packages Related to bowtie

• dep: libc6 (>= 2.11) [hppa]

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

  dep: libc6 (>= 2.16) [x32]

  dep: libc6 (>= 2.17) [sh4]

  dep: libc6 (>= 2.34) [not alpha, arm64, hppa, sh4, x32]

  dep: libc6 (>= 2.38) [arm64]

• dep: libc6.1 (>= 2.34) [alpha]

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

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

  GCC support library

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

• dep: libgcc1 [x32]

  Package not available

  dep: libgcc1 (>= 1:4.2.1) [sh4]

• dep: libgcc4 (>= 4.1.1) [hppa]

  Package not available

• dep: libstdc++6 [x32]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 13.1) [not arm64, hppa, sh4, x32]

  dep: libstdc++6 (>= 14) [arm64]

  dep: libstdc++6 (>= 4.4.0) [hppa, sh4]

• dep: python3 [not hppa, sh4, x32]

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

• dep: zlib1g (>= 1:1.2.6) [not hppa, sh4, x32]

  compression library - runtime

• sug: bowtie-examples

  Examples for bowtie, the ultrafast memory-efficient short read aligner

Download bowtie

Download for all available architectures

Architecture	Version	Package Size	Installed Size	Files
alpha (unofficial port)	1.3.1-3	1,333.8 kB	8,673.0 kB	[list of files]
amd64	1.3.1-3	1,588.9 kB	6,845.0 kB	[list of files]
arm64	1.3.1-3+b1	1,305.9 kB	6,738.0 kB	[list of files]
hppa (unofficial port)	1.0.0-6	894.0 kB	3,548.0 kB	[list of files]
mips64el	1.3.1-3	1,050.6 kB	8,129.0 kB	[list of files]
ppc64 (unofficial port)	1.3.1-3	1,328.0 kB	8,145.0 kB	[list of files]
ppc64el	1.3.1-3	1,370.8 kB	7,889.0 kB	[list of files]
riscv64	1.3.1-3	1,510.0 kB	5,365.0 kB	[list of files]
s390x	1.3.1-3	1,530.6 kB	6,969.0 kB	[list of files]
sh4 (unofficial port)	1.0.0-6	860.1 kB	3,077.0 kB	[list of files]
sparc64 (unofficial port)	1.3.1-3	1,149.4 kB	14,721.0 kB	[list of files]
x32 (unofficial port)	1.0.1-2	878.8 kB	3,264.0 kB	[list of files]