Source: qiime
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
           Tim Booth <tbooth@ceh.ac.uk>,
           Andreas Tille <tille@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
               dh-python,
               python3,
               python3-setuptools,
               python3-nose,
               python3-bibtexparser,
               python3-decorator,
               python3-pandas,
               python3-tzlocal,
               python3-yaml
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/qiime
Vcs-Git: https://salsa.debian.org/med-team/qiime.git
Homepage: https://qiime2.org

Package: qiime
Architecture: all
Depends: ${shlibs:Depends},
         ${misc:Depends},
         ${python3:Depends},
         python3-bibtexparser,
         python3-decorator,
         python3-matplotlib,
         python3-numpy,
         python3-pandas,
         python3-tzlocal,
         python3-yaml,
         python-burrito,
         python-burrito-fillings (>= 0.1.1),
         python-biom-format,
         python-cogent (>= 1.5.3),
         python-mpi4py,
         python-qcli,
         pynast (>= 1.2.2),
         qiime-data,
         ampliconnoise,
         blast2 | blast+-legacy,
         bwa,
         cd-hit,
         chimeraslayer,
         clearcut,
         clustalw,
         ea-utils,
         emperor (>= 0.9.51),
         fasttree,
         infernal,
         libjs-jquery,
         mafft,
         muscle,
         parsinsert,
         raxml,
         r-cran-optparse,
         rdp-classifier,
         seqprep,
         sortmerna,
         sumatra,
         swarm,
         vsearch
Recommends: mothur,
            rtax
Suggests: t-coffee,
          cytoscape,
          torque-client,
          qiime-default-reference
Description: 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.
 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.
