subread_1.5.0-p1+dfsg-2_i386.deb


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Description

subread - toolkit for processing next-gen sequencing data

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name subread
Package version 1.5.0
Package release p1+dfsg-2
Package architecture i386
Package type deb
Installed size 6.85 KB
Download size 542.38 KB
Official Mirror archive.ubuntu.com
Subread aligner can be used to align both gDNA-seq and RNA-seq reads.
Subjunc aligner was specified designed for the detection of exon-exon
junction. For the mapping of RNA-seq reads, Subread performs local
alignments and Subjunc performs global alignments.

Alternatives

Package Version Architecture Repository
subread_1.5.0-p1+dfsg-2_amd64.deb 1.5.0 amd64 Ubuntu Universe
subread - - -

Requires

Name Value
libc6 >= 2.15
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package subread_1.5.0-p1+dfsg-2_i386.deb
Source Package subread

Install Howto

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

Files

Path
/usr/bin/exactSNP
/usr/bin/featureCounts
/usr/bin/subindel
/usr/bin/subjunc
/usr/bin/subread-align
/usr/bin/subread-buildindex
/usr/lib/subread/coverageCount
/usr/lib/subread/propmapped
/usr/lib/subread/qualityScores
/usr/lib/subread/removeDup
/usr/lib/subread/repair
/usr/lib/subread/subread-fullscan
/usr/share/doc/subread/README.Debian
/usr/share/doc/subread/README.txt
/usr/share/doc/subread/changelog.Debian.gz
/usr/share/doc/subread/copyright
/usr/share/man/man1/coverageCount.1.gz
/usr/share/man/man1/exactSNP.1.gz
/usr/share/man/man1/featureCounts.1.gz
/usr/share/man/man1/propmapped.1.gz
/usr/share/man/man1/qualityScores.1.gz
/usr/share/man/man1/removeDup.1.gz
/usr/share/man/man1/repair.1.gz
/usr/share/man/man1/subindel.1.gz
/usr/share/man/man1/subjunc.1.gz
/usr/share/man/man1/subread-align.1.gz
/usr/share/man/man1/subread-buildindex.1.gz
/usr/share/man/man1/subread-fullscan.1.gz

Changelog

2016-01-18 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.5.0-p1+dfsg-2) unstable; urgency=medium
* d/control: remove hurd-i386 and mipsel due to failing tests
2016-01-05 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.5.0-p1+dfsg-1) unstable; urgency=medium
* Imported Upstream version 1.5.0-p1+dfsg
* d/patches: refresh and remove applied patches
2015-11-06 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.5.0+dfsg-1) unstable; urgency=medium
* Imported Upstream version 1.5.0+dfsg
* no PDF documentation in this release
* removed globalReassembly and subtools binaries, added "repair" tool
2015-09-05 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p5+dfsg-1) unstable; urgency=medium
* Imported Upstream version 1.4.6-p5+dfsg
* Build and install SubreadUsersGuide.pdf
2015-07-06 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p4+dfsg-1) unstable; urgency=medium
* d/patches/arch_specific_flags.patch: set the optimization level 
to -03  because -O levels higher than 3 have no effect.
* Imported Upstream version 1.4.6-p4+dfsg
2015-05-21 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p3+dfsg-2) unstable; urgency=medium
* d/changelog: upload to unstable, forgot to include the amd64 architecture 
in d/contorl
* d/control: added amd64 to Architecture
2015-05-19 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p3+dfsg-1) unstable; urgency=medium
* d/changelog: upload to unstable
* d/rules: enable -fsigned-char for all architectures
* d/patches/arch_specific_flags.patch: use -O2 instead of -O9
* d/control: not building for powerpc, mips, s390x, see d/README.source
* d/README.source: merge with d/README.Debian-source describe the reason
for not building on some architectures
* Imported Upstream version 1.4.6-p3+dfsg
2015-05-18 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p2+dfsg-4) experimental; urgency=medium
* d/rules: add -msse3 and -mtune=generic for i386/amd64 
* d/patches: merge hardening and gcc_flags_cleanup patches
* d/patches: updated and renamed getopt4exactSNP.patch to getopt.patch 
fixed 2 more issues with wrong assignment for the getopt_long function
2015-05-13 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p2+dfsg-3) experimental; urgency=medium
* d/patches/getopt4exactSNP.patch: attempt to fix #784929
2015-05-10 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
subread (1.4.6-p2+dfsg-2) unstable; urgency=medium
* d/patches/gcc_flags_cleanup.patch: remove -mtune=core2 and mmmx,msse* flags
Closes: #784780 
* d/rules: use override_dh_installexamples-indep, Closes: #784782 
* d/README.Debian-source: mention doc/SubreadUserGuide.pdf removal

See Also

Package Description
substance-doc_5.3-3_all.deb cross-platform look & feel for Swing applications - documentation
substance_5.3-3_all.deb cross-platform look & feel for Swing applications
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subtle_0.11.3224-xi-2.2_i386.deb grid-based manual tiling window manager
subunit_1.1.0-3_all.deb command line tools for processing Subunit streams
suck_4.3.2-15_i386.deb small newsfeed from an NNTP server with standard NNTP commands
suckless-tools_42-1_i386.deb simple commands for minimalistic window managers
sucrack_1.2.3-2ubuntu1_i386.deb multithreaded su bruteforcer
sucrose_0.106.1-1_all.deb Sugar Learning Platform - Sucrose
sudo-ldap_1.8.16-0ubuntu1_i386.deb Provide limited super user privileges to specific users
sudoku_1.0.5-2build1_i386.deb console based sudoku
sugar-browse-activity_157.2-2_all.deb Sugar Learning Platform - web browsing activity
sugar-calculate-activity_43-2_all.deb Sugar Learning Platform - calculation activity
sugar-chat-activity_81-4_all.deb Sugar Learning Platform - text chatting activity
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