mapsembler2_2.2.4+dfsg-1_amd64.deb


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Description

mapsembler2 - bioinformatics targeted assembly software

Property Value
Distribution Ubuntu 18.04 LTS (Bionic Beaver)
Repository Ubuntu Universe amd64
Package filename mapsembler2_2.2.4+dfsg-1_amd64.deb
Package name mapsembler2
Package version 2.2.4+dfsg
Package release 1
Package architecture amd64
Package type deb
Category universe/science
Homepage http://colibread.inria.fr/mapsembler2/
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 248.38 KB
Installed size 780.00 KB
Mapsembler2 is a targeted assembly software.
It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not)
and a set of input sequences (starters).
It first determines if each starter is read-coherent, e.g. whether reads
confirm the presence of each starter in the original sequence.
Then for each read-coherent starter, Mapsembler2 outputs its sequence
neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):
- Validate an assembled sequence (input as starter), e.g. from a de
Bruijn graph assembly where read-coherence was not enforced.
- Checks if a gene (input as starter) has an homolog in a set of reads
- Checks if a known enzyme is present in a metagenomic NGS read set.
- Enrich unmappable reads by extending them, possibly making them mappable
- Checks what happens at the extremities of a contig
- Remove contaminants or symbiont reads from a read set

Alternatives

Package Version Architecture Repository
mapsembler2_2.2.4+dfsg-1_i386.deb 2.2.4+dfsg i386 Ubuntu Universe
mapsembler2 - - -

Requires

Name Value
bc -
libc6 >= 2.14
libgcc1 >= 1:3.0
libgomp1 >= 4.9
libstdc++6 >= 5.2
zlib1g >= 1:1.2.3.4

Download

Type URL
Mirror archive.ubuntu.com
Binary Package mapsembler2_2.2.4+dfsg-1_amd64.deb
Source Package mapsembler2

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install mapsembler2 deb package:
    # sudo apt-get install mapsembler2

Files

Path
/usr/bin/mapsembler2_extremities
/usr/bin/mapsembler2_kissreads
/usr/bin/mapsembler2_kissreads_graph
/usr/bin/mapsembler_extend
/usr/bin/run_mapsembler2_pipeline
/usr/share/doc/mapsembler2/README.Debian
/usr/share/doc/mapsembler2/changelog.Debian.gz
/usr/share/doc/mapsembler2/copyright
/usr/share/man/man1/mapsembler2_extremities.1.gz
/usr/share/man/man1/mapsembler2_kissreads.1.gz
/usr/share/man/man1/mapsembler2_kissreads_graph.1.gz
/usr/share/man/man1/mapsembler_extend.1.gz
/usr/share/man/man1/run_mapsembler2_pipeline.1.gz

Changelog

2017-09-26 - Andreas Tille <tille@debian.org>
mapsembler2 (2.2.4+dfsg-1) unstable; urgency=medium
* New upstream version
* Moved packaging from SVN to Git
* d/watch:
- version=4
- fix URL
- recompression with xz
* debhelper 10
* Standards-Version: 4.1.0 (no changes needed)
2016-09-09 - Andreas Tille <tille@debian.org>
mapsembler2 (2.2.3+dfsg-3) unstable; urgency=medium
* Fix type of prefix_trashable since gcc-5 is picky about it (Thanks to
Gianfranco Costamagna <costamagnagianfranco@yahoo.it> for the hint)
Closes: #797526
* cme fix dpkg-control
* DEP5 syntax
* hardening=+all
[ Olivier Sallou ]
* d/copyright: add Upstream-Contact
2014-10-26 - Andreas Tille <tille@debian.org>
mapsembler2 (2.2.3+dfsg-2) unstable; urgency=medium
* Some DEP5 fixes
* Fix clean target
Closes: #766791
* cme fix dpkg-control
* [O. Sallou] d/control: limit target archs, upstream code uses some code
not valid on other archs, could not find an appropriate patch for this
(lower #765285 to normal).
2014-09-19 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.2.3+dfsg-1) unstable; urgency=medium
* New upstream release
* Fix some compilation issues 
* Fix FTBS on non x86 (Closes: #765285).
2014-08-20 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.2.1+dfsg-3) unstable; urgency=medium
[Gilles Filippini <pini@debian.org> ]
* Support hdf5 1.8.13 new packaging layout (Closes: #758730).
* Fix FTBFS due to broken help2man call in debian/rules.
2014-08-19 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.2.1+dfsg-2) unstable; urgency=medium
* Fix kissreads file conflict with discoSnp (Closes: #758648).
2014-05-29 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.2.1+dfsg-1) unstable; urgency=medium
* New upstream release
Change of license to AGPL-3
2014-02-21 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.1.2+dfsg-1) unstable; urgency=low
* New upstream release
2014-02-21 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.0.31-1) unstable; urgency=low
* New upstream release 
2014-02-06 - Olivier Sallou <osallou@debian.org>
mapsembler2 (2.0.5+dfsg-2) unstable; urgency=low
* d/control: Add missing build dep

See Also

Package Description
mapserver-bin_7.0.7-1build2_amd64.deb MapServer utilities
mapserver-doc_7.0.7-1build2_all.deb documentation for MapServer
maptool_0.5.0+dfsg.1-2build1_amd64.deb Converts OpenStreetMap maps to Navit
maptransfer-server_0.3-2_all.deb upload/download maps to/from a VALVe game server (Server)
maptransfer_0.3-2_all.deb upload/download maps to/from a VALVe game server (Client)
maq_0.7.1-7_amd64.deb maps short fixed-length polymorphic DNA sequence reads to reference sequences
maqview_0.2.5-8_amd64.deb graphical read alignment viewer for short gene sequences
maradns-deadwood_2.0.13-1.2_amd64.deb simple security-focused recursive Domain Name Service server
maradns-docs_2.0.13-1.2_all.deb upstream documentation for the MaraDNS Domain Name Service server
maradns-zoneserver_2.0.13-1.2_amd64.deb complementary server process to TCP functions for MaraDNS
maradns_2.0.13-1.2_amd64.deb simple security-focused authoritative Domain Name Service server
marble-data_17.12.3-0ubuntu1_all.deb data files for Marble
marble-maps_17.12.3-0ubuntu1_amd64.deb globe and map widget for mobile form factors
marble-plugins_17.12.3-0ubuntu1_amd64.deb plugins for Marble
marble-qt_17.12.3-0ubuntu1_amd64.deb globe and map widget (no KDE dependencies)
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