qiime 1.8.0+dfsg-2 source package in Ubuntu

Changelog

qiime (1.8.0+dfsg-2) unstable; urgency=medium


  * debian/qiime.links: Fix links to new biom_format
  * debian/control:
     - New dependency: python-qcli (this should be dropped in version
       2.0 of qiime)
     - Recommends: python-mpi4py since this is used in some tests
  * debian/rules: Remove remainings from running test suite

 -- Andreas Tille <email address hidden>  Thu, 26 Dec 2013 07:39:57 +0100

Upload details

Uploaded by:
Debian Med on 2013-12-30
Uploaded to:
Sid
Original maintainer:
Debian Med
Architectures:
any all
Section:
science
Urgency:
Medium Urgency

See full publishing history Publishing

Series Pocket Published Component Section
Trusty release on 2013-12-30 universe science

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File Size SHA-256 Checksum
qiime_1.8.0+dfsg-2.dsc 1.5 KiB cf6e5ee248c27bb92a5aa4ff459aadfd9b29035f93b0381dd461eb33a29b4a26
qiime_1.8.0+dfsg.orig.tar.xz 14.0 MiB cb9572d566a793ebaf47ecca4de0df895a991e97986594554cb927bb48d06a79
qiime_1.8.0+dfsg-2.debian.tar.gz 21.4 KiB 0f5b9479019dd985005ce8ac2ec30ab011bf3d74d60db415548b4de75922af0d

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Binary packages built by this source

qiime: Quantitative Insights Into Microbial Ecology

 QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
 microbial community analysis that integrates many third party tools which
 have become standard in the field. A standard QIIME analysis begins with
 sequence data from one or more sequencing platforms, including
  * Sanger,
  * Roche/454, and
  * Illumina GAIIx.
 With all the underlying tools installed,
 of which not all are yet available in Debian (or any other Linux
 distribution), QIIME can perform
  * library de-multiplexing and quality filtering;
  * denoising with PyroNoise;
  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
    or other tools;
  * taxonomy assignment with BLAST or the RDP classifier;
  * sequence alignment with PyNAST, muscle, infernal, or other tools;
  * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
  * alpha diversity and rarefaction, including visualization of results,
    using over 20 metrics including Phylogenetic Diversity, chao1, and
    observed species;
  * beta diversity and rarefaction, including visualization of results,
    using over 25 metrics including weighted and unweighted UniFrac,
    Euclidean distance, and Bray-Curtis;
  * summarization and visualization of taxonomic composition of samples
    using pie charts and histograms
 and many other features.
 .
 QIIME includes parallelization capabilities for many of the
 computationally intensive steps. By default, these are configured to
 utilize a mutli-core environment, and are easily configured to run in
 a cluster environment. QIIME is built in Python using the open-source
 PyCogent toolkit. It makes extensive use of unit tests, and is highly
 modular to facilitate custom analyses.

qiime-doc: Quantitative Insights Into Microbial Ecology (tutorial)

 QIIME (canonically pronounced ‘Chime’) is a pipeline for performing
 microbial community analysis that integrates many third party tools which
 have become standard in the field. A standard QIIME analysis begins with
 sequence data from one or more sequencing platforms, including
  * Sanger,
  * Roche/454, and
  * Illumina GAIIx.
 With all the underlying tools installed,
 of which not all are yet available in Debian (or any other Linux
 distribution), QIIME can perform
  * library de-multiplexing and quality filtering;
  * denoising with PyroNoise;
  * OTU and representative set picking with uclust, cdhit, mothur, BLAST,
    or other tools;
  * taxonomy assignment with BLAST or the RDP classifier;
  * sequence alignment with PyNAST, muscle, infernal, or other tools;
  * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
  * alpha diversity and rarefaction, including visualization of results,
    using over 20 metrics including Phylogenetic Diversity, chao1, and
    observed species;
  * beta diversity and rarefaction, including visualization of results,
    using over 25 metrics including weighted and unweighted UniFrac,
    Euclidean distance, and Bray-Curtis;
  * summarization and visualization of taxonomic composition of samples
    using pie charts and histograms
 and many other features.
 .
 QIIME includes parallelization capabilities for many of the
 computationally intensive steps. By default, these are configured to
 utilize a mutli-core environment, and are easily configured to run in
 a cluster environment. QIIME is built in Python using the open-source
 PyCogent toolkit. It makes extensive use of unit tests, and is highly
 modular to facilitate custom analyses.
 .
 This package contains the documentation and a tutorial.