mapsembler2_2.1.6+dfsg-1_amd64.deb


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Description

mapsembler2 - bioinformatics targeted assembly software

Distribution: Debian 8 (Jessie)
Repository: Debian Main amd64
Package name: mapsembler2
Package version: 2.1.6+dfsg
Package release: 1
Package architecture: amd64
Package type: deb
Installed size: 454 B
Download size: 272.52 KB
Official Mirror: ftp.br.debian.org
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

    Download

    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

    • /usr/bin/mapsembler
    • /usr/share/doc/mapsembler2/README.Debian
    • /usr/share/doc/mapsembler2/changelog.Debian.gz
    • /usr/share/doc/mapsembler2/copyright
    • /usr/share/doc/mapsembler2/sample_example/fragments.fa
    • /usr/share/doc/mapsembler2/sample_example/reads.fa.gz
    • /usr/share/man/man1/mapsembler.1.gz

    Changelog

    2014-05-29 - Olivier Sallou <osallou@debian.org> mapsembler2 (2.1.6+dfsg-1) unstable; urgency=medium * New upstream release

    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

    2014-02-01 - Olivier Sallou <osallou@debian.org> mapsembler2 (2.0.5+dfsg-1) unstable; urgency=medium * First debian package (Closes: #737099).

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