Delete old Qiime dependencies

qiime (2019.1.0-2) UNRELEASED; urgency=medium

  * Team upload.

  * Delete old Qiime dependencies

 -- Liubov Chuprikova <chuprikovalv@gmail.com>  Tue, 12 Mar 2019 00:13:16 +0200

qiime (2019.1.0-1) unstable; urgency=medium

  [ Andreas Tille ]

         ${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

         python3-pyparsing,

         python3-dateutil

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 2 is a powerful, extensible, and decentralized microbiome analysis

 package with a focus on data and analysis transparency. QIIME 2 enables

 researchers to start an analysis with raw DNA sequence data and finish with

 publication-quality figures and statistical results.

 Key features:

  * Integrated and automatic tracking of data provenance

  * Semantic type system

  * Plugin system for extending microbiome analysis functionality

  * Support for multiple types of user interfaces (e.g. API, command line,

 graphical)

 .

 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 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis

 pipeline. QIIME 2 will address many of the limitations of QIIME 1, while

 retaining the features that makes QIIME 1 a powerful and widely-used analysis

 pipeline.

 .

 QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline.

 New functionality will regularly become available through QIIME 2 plugins. You

 can view a list of plugins that are currently available on the QIIME 2 plugin

 availability page. The future plugins page lists plugins that are being

 developed.