bowtie-examples_1.1.1-2_all.deb


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Description

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

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main i386
Package name bowtie-examples
Package version 1.1.1
Package release 2
Package architecture all
Package type deb
Installed size 6.62 KB
Download size 6.02 MB
Official Mirror ftp.br.debian.org
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).
This package provides some example data to work with bowtie.

Alternatives

Package Version Architecture Repository
bowtie-examples_1.1.1-2_all.deb 1.1.1 all Debian Main
bowtie-examples - - -

Download

Type URL
Binary Package bowtie-examples_1.1.1-2_all.deb
Source Package bowtie

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install bowtie-examples deb package:
    # sudo apt-get install bowtie-examples

Files

Path
/usr/share/doc/bowtie-examples/changelog.Debian.gz
/usr/share/doc/bowtie-examples/copyright
/usr/share/doc/bowtie/examples/genomes/NC_008253.fna.gz
/usr/share/doc/bowtie/examples/indexes/e_coli.1.ebwt
/usr/share/doc/bowtie/examples/indexes/e_coli.2.ebwt
/usr/share/doc/bowtie/examples/indexes/e_coli.3.ebwt
/usr/share/doc/bowtie/examples/indexes/e_coli.4.ebwt
/usr/share/doc/bowtie/examples/indexes/e_coli.README
/usr/share/doc/bowtie/examples/indexes/e_coli.rev.1.ebwt
/usr/share/doc/bowtie/examples/indexes/e_coli.rev.2.ebwt

Changelog

2015-02-03 - Charles Plessy <plessy@debian.org>
bowtie (1.1.1-2) unstable; urgency=high
* Team upload.
* Install missing commands.  Closes: #776881.
2014-10-02 - Andreas Tille <tille@debian.org>
bowtie (1.1.1-1) unstable; urgency=medium
* New upstream release
* cme fix dpkg-control
* Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
* Add Depends: python (also Build-Depends since it is used in tests)
2014-09-15 - Andreas Tille <tille@debian.org>
bowtie (1.0.1-3) unstable; urgency=medium
* Drop all architectures except amd64 since there was no success
in trying to port the code to other architectures.  The portability
patch introduced in the last revision was droped again
* debian/copyright: Drop unneeded copyright statements about code that
was removed from upstream source
2014-09-03 - Andreas Tille <tille@debian.org>
bowtie (1.0.1-2) unstable; urgency=medium
* Do not use copy of outdated gcc header file which destroys portability
to other architectures
Closes: #756780
* Add README.Debian informing users about the fact that we ignore copy
of cpuid.h
* Add unit tests for build time and autopkgtest
* Add debian/README.test to explain how to test the package
Attention: Please take notice of /usr/share/bowtie/README.Debian about
"Test suite for bowtie created and potential issue with sorting"
2014-07-30 - Andreas Tille <tille@debian.org>
bowtie (1.0.1-1) unstable; urgency=medium
* New upstream version (adapted patches)
* drop debian/get-orig-source but rather remove the SeqAn-1.1 code
copy via Files-Excluded
* debian/control: Priority: optional
2014-03-08 - Ognyan Kulev <ogi@debian.org>
bowtie (1.0.0-6) unstable; urgency=low
* debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
* Version 1.4 of seqan-dev is required now.
* Standards-Version: 3.9.5 (no changes needed).
* Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.
2013-05-30 - Ognyan Kulev <ogi@debian.org>
bowtie (1.0.0-5) unstable; urgency=low
* Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
instead of override_dh_fixperms in debian/rules.
2013-05-29 - Ognyan Kulev <ogi@debian.org>
bowtie (1.0.0-4) unstable; urgency=low
* Lintian fixes:
- Removed DM-Upload-Allowed field.
- Standards Version 3.9.4 (no changes needed).
- Remove execute bits on some files in bowtie-examples.
* Don't compress *.ebwt index files in bowtie-examples package.
* Package description now starts with a capital letter.
2013-04-24 - Ognyan Kulev <ogi@debian.org>
bowtie (1.0.0-3) unstable; urgency=low
* New patch no_hash_style_both_for_mips.patch.
This fixes build errors on mips and mipsel.
2013-04-24 - Ognyan Kulev <ogi@debian.org>
bowtie (1.0.0-2) unstable; urgency=low
* Requires version 1.3 of SeqAn.
* Updated README.source about using Debian's SeqAn library.
* Removed machine_bits_detection.patch and added disable_bits_flag.patch.

See Also

Package Description
bowtie2-examples_2.2.4-1_all.deb Examples for bowtie2
boxbackup-client_0.11.1~r2837-1_i386.deb client for the BoxBackup remote backup system
boxbackup-server_0.11.1~r2837-1_i386.deb server for the BoxBackup remote backup system
boxer-data_6_all.deb classes and nodes usable by Boxer
boxer_0.003-2_all.deb system deployment ninja tricks
boxes_1.1.1-4_i386.deb textmode box- and comment drawing filter
boxshade_3.3.1-8_i386.deb Pretty-printing of multiple sequence alignments
bplay_0.991-10_i386.deb Buffered audio file player/recorder
bpm-tools_0.3-1_i386.deb command-line tool to calculate tempo of audio
bppphyview_0.3.0-1_i386.deb Bio++ Phylogenetic Viewer
bpython-gtk_0.12-1.2_all.deb fancy interface to the Python interpreter - GTK+ frontend
bpython-urwid_0.12-1.2_all.deb fancy interface to the Python interpreter - urwid frontend
bpython3_0.12-1.2_all.deb fancy interface to the Python3 interpreter - Curses frontend
bpython_0.12-1.2_all.deb fancy interface to the Python interpreter - Curses frontend
br2684ctl_2.5.1-1.5_i386.deb Utility for configuring RFC 2684 ATM/Ethernet bridging
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