chimeraslayer_20101212+dfsg1-2_all.deb


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Description

chimeraslayer - detects likely chimeras in PCR amplified DNA

Property Value
Distribution Debian 10 (Buster)
Repository Debian Main i386
Package filename chimeraslayer_20101212+dfsg1-2_all.deb
Package name chimeraslayer
Package version 20101212+dfsg1
Package release 2
Package architecture all
Package type deb
Category biology::nucleic-acids field::biology science
Homepage http://microbiomeutil.sourceforge.net/
License -
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Download size 32.94 KB
Installed size 155.00 KB
ChimeraSlayer is a chimeric sequence detection utility, compatible with
near-full length Sanger sequences and shorter 454-FLX sequences (~500bp).
Chimera Slayer involves the following series of steps that operate to
flag chimeric 16S rRNA sequences:
1. the ends of a query sequence are searched against an included
database of reference chimera-free 16S sequences to identify potential
parents of a chimera
2. candidate parents of a chimera are selected as those that form a
branched best scoring alignment to the NAST-formatted query sequence
3. the NAST alignment of the query sequence is improved in a
‘chimera-aware’ profile-based NAST realignment to the selected
reference parent sequences
4. an evolutionary framework is used to flag query sequences found to
exhibit greater sequence homology to an in silico chimera formed
between any two of the selected reference parent sequences.
To run Chimera Slayer, you need NAST-formatted sequences generated by
the nast-ier utility.
ChimeraSlayer is part of the microbiomeutil suite.

Alternatives

Package Version Architecture Repository
chimeraslayer_20101212+dfsg1-2_all.deb 20101212+dfsg1 all Debian Main
chimeraslayer - - -

Requires

Name Value
blast2 -
cdbfasta -
microbiomeutil-data -

Download

Type URL
Mirror ftp.br.debian.org
Binary Package chimeraslayer_20101212+dfsg1-2_all.deb
Source Package microbiomeutil

Install Howto

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

Files

Path
/usr/bin/chimeraslayer
/usr/lib/ChimeraSlayer/ChimeraSlayer.pl
/usr/lib/ChimeraSlayer/ChimeraParentSelector/CM_plotter.pl
/usr/lib/ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl
/usr/lib/ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl
/usr/lib/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl
/usr/lib/ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl
/usr/lib/ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl
/usr/lib/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl
/usr/lib/ChimeraSlayer/PerlLib/AlignCompare.pm
/usr/lib/ChimeraSlayer/PerlLib/BHStats.pm
/usr/lib/ChimeraSlayer/PerlLib/CdbTools.pm
/usr/lib/ChimeraSlayer/PerlLib/Fasta_reader.pm
/usr/lib/ChimeraSlayer/PerlLib/NAST_to_Eco_coords.pm
/usr/lib/ChimeraSlayer/PerlLib/TaxonomyGraph.pm
/usr/lib/ChimeraSlayer/util/CMCS_to_treeImg.pl
/usr/lib/ChimeraSlayer/util/CS_add_taxonomy.pl
/usr/lib/ChimeraSlayer/util/breakpoint_to_profile.pl
/usr/lib/ChimeraSlayer/util/merge_CM_CS_outputs.pl
/usr/lib/ChimeraSlayer/util/merge_CS_n_CM_breakpoints.pl
/usr/share/doc/chimeraslayer/changelog.Debian.gz
/usr/share/doc/chimeraslayer/copyright
/usr/share/doc/chimeraslayer/examples
/usr/share/man/man1/chimeraslayer.1.gz

Changelog

2018-07-05 - Andreas Tille <tille@debian.org>
microbiomeutil (20101212+dfsg1-2) unstable; urgency=low
[ Steffen Moeller ]
* debian/upstream/metadata:
- Added references to registries
- yamllint cleanliness
[ Andreas Tille ]
* Remove unneeded get-orig-source target
* Remove Tim Booth from Uploaders (thanks for your work, Tim)
* Secure URI in watch file
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* hardening=+all
2016-01-20 - Andreas Tille <tille@debian.org>
microbiomeutil (20101212+dfsg1-1) unstable; urgency=low
* debian/copyright: s/BSD-like/BSD-3-clause/
* Moved debian/upstream to debian/upstream/metadata
* cme fix dpkg-control
* Cleanup d/rules
* Fix build time tests and run these
* Add doc-base file
* d/watch: add missing repacksuffix
* Moved packaging from SVN to Git
* Cleaning up log files from past test runs
* Add autopkgtest
2013-07-22 - Andreas Tille <tille@debian.org>
microbiomeutil (20101212+dfsg-1) unstable; urgency=low
* Initial release to Debian (Closes: #711086)
* Remove copyrighted logo images from upstream tarball (the logo is
only used in very short doc which works perfectly without this image)
* debian/control: Use anonscm Vcs addresses
2013-06-05 - Tim Booth <tbooth@ceh.ac.uk>
microbiomeutil (20101212-1ubuntu8) precise; urgency=low
* Bio-Linux rebuild with Andreas' fixes  
* ChimeraSlayer run from QIIME was not working.  Need to pre-compute
index files and add them to RESOURCES directory
* Also added missing direct dep on blast2
2013-06-04 - Andreas Tille <tille@debian.org>
microbiomeutil (20101212-2) unstable; urgency=low
* debian/copyright: DEP5 copyright
* debian/control:
- Added myself to uploaders
- Priority: optional (as per Debian Med policy)
- Droped DM-Upload-Allowed
- Standards-Version: 3.9.4
- Debhelper 9 (also d/compat)
- Dropped explicit quilt Build-Dependends
- better formatting
- Enhance long descriptions
* debian/rules:
- remove "--with quilt" because this is specified in source format
- Use xz compression for binaries
* debian/rules, debian/*.install, debian/*.links:
Rather use the usual debhelper input files
* Remove unneeded debian/README.* files and create debian/upstream
file with citation information
* Removed debian/{ChimeraSlayer,microbiomeutil.install} because
unneeded
* debian/*.1: Wrote manpages
* debian/microbiomeutil.links: Synonyms with camel case spelling
as in the provided documentation
* debian/patches/hardening.patch: Enable propagation of hardening options
2013-06-03 - Tim Booth <tbooth@ceh.ac.uk>
microbiomeutil (20101212-1ubuntu6) lucid; urgency=low
* Another patch needed to Perl code due to inappropriate use of
FindBin 
* Move to /usr/lib rather than /usr/share as per Lintian warnings.
* Set --with quilt on dh.  (Possibly not needed now?)
* Added better descriptions in debian/control
2011-04-11 - Tim Booth <tbooth@ceh.ac.uk>
microbiomeutil (20101212-1ubuntu1) lucid; urgency=low
* Split package into 4 binary packages.
2011-03-30 - Steffen Moeller <moeller@debian.org>
microbiomeutil (2010-11-1) UNRELEASED; urgency=low
* New upstream
2010-12-02 - Steffen Moeller <moeller@debian.org>
microbiomeutil (2010-11-02-1) UNRELEASED; urgency=low
* Initial packaging

See Also

Package Description
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chkservice_0.1-3_i386.deb Tool for managing systemd units
chktex_1.7.6-2+b1_i386.deb Finds typographic errors in LaTeX
chm2pdf_0.9.1-1.2_all.deb A Python script that converts CHM files into PDF files
chntpw_1.0-1.1_i386.deb NT SAM password recovery utility
chocolate-common_3.0.0-4_all.deb dummy transitional package for chocolate-doom related packages
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choosewm_0.1.6-3+b2_i386.deb fake x-session-manager allowing the user to choose a wm
choqok_1.6-2.1_i386.deb KDE micro-blogging client
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