ampliconnoise_1.29-2_amd64.deb


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Description

ampliconnoise - removal of noise from 454 sequenced PCR amplicons

Property Value
Distribution Debian 8 (Jessie)
Repository Debian Main amd64
Package name ampliconnoise
Package version 1.29
Package release 2
Package architecture amd64
Package type deb
Installed size 1.30 KB
Download size 455.89 KB
Official Mirror ftp.br.debian.org
AmpliconNoise is a package of applications to clean up high-throughput
sequence data.  It consists of three main parts:
Pyronoise - does flowgram-based clustering to spot misreads
SeqNoise - removes PCR point mutations
Perseus - removes PCR chimeras without the need for a set of reference
sequences
Previously there was a standalone "Pyronoise" by the same authors and
this package includes an updated version.  There is also a "Denoiser"
in Qiime which is related but distinct.

Alternatives

Package Version Architecture Repository
ampliconnoise_1.29-2_i386.deb 1.29 i386 Debian Main
ampliconnoise - - -

Requires

Name Value
libc6 >= 2.14
libgsl0ldbl >= 1.9
libhwloc5 -
libopenmpi1.6 -
mafft -

Download

Type URL
Binary Package ampliconnoise_1.29-2_amd64.deb
Source Package ampliconnoise

Install Howto

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

Files

Path
/usr/bin/FCluster
/usr/bin/FastaUnique
/usr/bin/NDist
/usr/bin/Perseus
/usr/bin/PerseusD
/usr/bin/PyroDist
/usr/bin/PyroNoise
/usr/bin/PyroNoiseA
/usr/bin/PyroNoiseM
/usr/bin/SeqDist
/usr/bin/SeqNoise
/usr/bin/SplitClusterClust
/usr/bin/SplitClusterEven
/usr/share/ampliconnoise/Data/LookUp.dat
/usr/share/ampliconnoise/Data/LookUp_E123.dat
/usr/share/ampliconnoise/Data/LookUp_Titanium.dat
/usr/share/ampliconnoise/Data/Tran.dat
/usr/share/ampliconnoise/Data/TranN.dat
/usr/share/ampliconnoise/Data/Tran_D.dat
/usr/share/ampliconnoise/Data/Tran_V6.dat
/usr/share/ampliconnoise/Scripts/CSV.pl
/usr/share/ampliconnoise/Scripts/Class.pl
/usr/share/ampliconnoise/Scripts/Clean.sh
/usr/share/ampliconnoise/Scripts/Clean360.pl
/usr/share/ampliconnoise/Scripts/CleanAcyclic.pl
/usr/share/ampliconnoise/Scripts/CleanBoth.pl
/usr/share/ampliconnoise/Scripts/CleanBothM.pl
/usr/share/ampliconnoise/Scripts/CleanMinMax.pl
/usr/share/ampliconnoise/Scripts/CleanMinMax.sh
/usr/share/ampliconnoise/Scripts/ConvertDatFasta.pl
/usr/share/ampliconnoise/Scripts/CountFasta.pl
/usr/share/ampliconnoise/Scripts/CountSequences.pl
/usr/share/ampliconnoise/Scripts/Diversity.pl
/usr/share/ampliconnoise/Scripts/FilterGoodClass.pl
/usr/share/ampliconnoise/Scripts/FlowsFA.pl
/usr/share/ampliconnoise/Scripts/FlowsFA360.pl
/usr/share/ampliconnoise/Scripts/FlowsMinMax.pl
/usr/share/ampliconnoise/Scripts/Join.pl
/usr/share/ampliconnoise/Scripts/Map.pl
/usr/share/ampliconnoise/Scripts/MedianS.sh
/usr/share/ampliconnoise/Scripts/Parse.pl
/usr/share/ampliconnoise/Scripts/ParseBoth.pl
/usr/share/ampliconnoise/Scripts/Qiime.pl
/usr/share/ampliconnoise/Scripts/Qiime_OTU.pl
/usr/share/ampliconnoise/Scripts/Qiime_Typical.pl
/usr/share/ampliconnoise/Scripts/RunBoth.sh
/usr/share/ampliconnoise/Scripts/RunBothFLX.sh
/usr/share/ampliconnoise/Scripts/RunFLX.sh
/usr/share/ampliconnoise/Scripts/RunTitanium.sh
/usr/share/ampliconnoise/Scripts/RunTitaniumA.sh
/usr/share/ampliconnoise/Scripts/RunTitaniumFast.sh
/usr/share/ampliconnoise/Scripts/RunTitaniumWeb.sh
/usr/share/ampliconnoise/Scripts/Split.pl
/usr/share/ampliconnoise/Scripts/SplitKeys.pl
/usr/share/ampliconnoise/Scripts/SplitKeysBoth.pl
/usr/share/ampliconnoise/Scripts/SplitKeysFlower.pl
/usr/share/ampliconnoise/Scripts/Sub.pl
/usr/share/ampliconnoise/Scripts/Subsample.sh
/usr/share/ampliconnoise/Scripts/SubsampleDat.pl
/usr/share/ampliconnoise/Scripts/Truncate.pl
/usr/share/ampliconnoise/Scripts/Typical.pl
/usr/share/doc-base/ampliconnoise
/usr/share/doc/ampliconnoise/Doc.pdf
/usr/share/doc/ampliconnoise/README.Debian
/usr/share/doc/ampliconnoise/changelog.Debian.gz
/usr/share/doc/ampliconnoise/copyright
/usr/share/man/man1/FCluster.1.gz
/usr/share/man/man1/FastaUnique.1.gz
/usr/share/man/man1/NDist.1.gz
/usr/share/man/man1/Perseus.1.gz
/usr/share/man/man1/PerseusD.1.gz
/usr/share/man/man1/PyroDist.1.gz
/usr/share/man/man1/PyroNoise.1.gz
/usr/share/man/man1/PyroNoiseA.1.gz
/usr/share/man/man1/PyroNoiseM.1.gz
/usr/share/man/man1/SeqDist.1.gz
/usr/share/man/man1/SeqNoise.1.gz
/usr/share/man/man1/SplitClusterClust.1.gz
/usr/share/man/man1/SplitClusterEven.1.gz
/usr/share/man/man1/ampliconnoise.1.gz

Changelog

2014-02-25 - Andreas Tille <tille@debian.org>
ampliconnoise (1.29-2) unstable; urgency=low
[ Arthur Marble ]
* Fix the FTBFS with clang:
- Fixed the non-void function should return a value in
FCluster/FCluster.c
SplitClusterEven/SplitClusterEven.c
Closes: #740029
[ James McCoy ]
* Moved debian/upstream to debian/upstream/metadata
2014-01-12 - Andreas Tille <tille@debian.org>
ampliconnoise (1.29-1) unstable; urgency=medium
* New upstream version
* debian/control:
- cme fix dpkg-control
- shorter short decription
2013-07-30 - Andreas Tille <tille@debian.org>
ampliconnoise (1.28-1) unstable; urgency=low
* New upstream version uploaded to Debian
* debian/control
- cme fix dpkg-control
- no need to Build-Depend from quilt
- debhelper 9
- Priority: optional
- Normalised Vcs fields
- Remove duplicated publication information from
long description
* debian/get-orig-source: Removed because upstream
stripped off their tarball
* debian/README.source: Removed because it became now
unneeded.
* debian/doc-base: created
* debian/rules:
- do not compress pdf files
* debian/patches/hardening.patch: Propagate hardening options
2013-06-27 - Tim Booth <tbooth@ceh.ac.uk>
ampliconnoise (1.28-0ubuntu2) precise; urgency=low
* Apply patch for segfault on attempt to load non-FASTA files 
2013-03-14 - Tim Booth <tbooth@ceh.ac.uk>
ampliconnoise (1.28-0ubuntu1) precise; urgency=low
* New upstream
* Upstream tarball now free of junk so using pristine version
* MPI versions of most things have now vanished
2012-05-16 - Andreas Tille <tille@debian.org>
ampliconnoise (1.25-2) UNRELEASED; urgency=low
* debian/upstream: Add citation information
* debian/watch: Fixed googlecode URL
* debian/copyright:
- DEP5
- Add Files-Excluded to document what was removed from original source
2011-08-21 - Tim Booth <tbooth@ceh.ac.uk>
ampliconnoise (1.25-1) unstable; urgency=low
[ Steffen sponsoring Tim's update ]
* Removed Steffen from uploader's list
* Removing emacs-typical backup files from source tree
2011-08-17 - Tim Booth <tbooth@ceh.ac.uk>
ampliconnoise (1.25-1) lucid; urgency=low
* Rebuild for new version - minor fix from upstream
2011-07-11 - Andreas Tille <tille@debian.org>
ampliconnoise (1.24-1) unstable; urgency=low
* debian/watch: Use googlecode.debian.net to make sure the
source tarball will be really found
* debian/get-orig-source: Make sure temporary dir will be
created, less noisy
* debian/copyright: DEP5 format
2011-07-07 - Tim Booth <tbooth@ceh.ac.uk>
ampliconnoise (1.24-1ubuntu2) lucid; urgency=low
* Fix build to use OpenMPI explicitly. Explicitly made build use
mpicc.openmpi even if MPICH2 is installed and set as default.
* More tweaks to ugly tarball repacking.

See Also

Package Description
amqp-specs_1-0r0-2_all.deb specs for the Advanced Message Queuing Protocol (AMQP)
amqp-tools_0.5.2-2_amd64.deb Command-line utilities for interacting with AMQP servers
ams_2.1.1-1_amd64.deb Realtime modular synthesizer for ALSA
amsn-data_0.98.9-1_all.deb Data files for aMSN
amsn_0.98.9-1+b1_amd64.deb MSN messenger application written in Tcl
amsynth_1.4.2-2_amd64.deb two oscillator software synthesizer
amtterm_1.3-2_amd64.deb Serial-over-lan (sol) client for Intel AMT, console version
amule-emc_0.5.2-3_amd64.deb lists ed2k links inside emulecollection files
an_1.2-1_amd64.deb very fast anagram generator
anacron_2.3-23_amd64.deb cron-like program that doesn't go by time
analitza-common_4.14.0-1_all.deb common files for Analitza
analog_6.0-20+b2_amd64.deb web server log analyzer
anarchism_14.0-3_all.deb Exhaustive exploration of Anarchist theory and practice
and_1.2.2-4.1_amd64.deb Auto Nice Daemon
android-androresolvd_1.3-1_amd64.deb Daemon to transfer Android DNS property to resolv.conf
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