Metadata-Version: 1.1
Name: micca
Version: 1.3.0
Summary: micca - MICrobial Community Analysis
Home-page: www.micca.org
Author: Davide Albanese
Author-email: davide.albanese@fmach.it
License: GPLv3
Download-URL: www.micca.org
Description: micca - MICrobial Community Analysis
        ====================================
        
        .. image:: https://travis-ci.org/compmetagen/micca.svg?branch=master
            :target: https://travis-ci.org/compmetagen/micca
        
        micca (MICrobial Community Analysis) is a software pipeline for the
        processing of amplicon sequencing data, **from raw sequences** to
        **OTU tables**, **taxonomy classification** and **phylogenetic tree**
        inference. The pipeline can be applied to a range of highly conserved
        genes/spacers, such as **16S rRNA gene**, **Internal Transcribed
        Spacer (ITS)** and **28S rRNA**.
        
        micca is an open-source, GPLv3-licensed software.
        
        * `Homepage <http://micca.org/>`_
        * `Documentation (latest) <http://micca.org/docs/latest>`_
        * `Issues <https://github.com/compmetagen/micca/issues>`_
        * `Github page <https://github.com/compmetagen/micca>`_
        
        
        Key features
        ------------
        
        * supports **single-end** (Roche 454, Illumina MiSeq/HiSeq ,Ion
          Torren) as well **overlapping paired-end** reads (Illumina MiSeq/HiSeq);
        * **multithread** de novo greedy clustering
        * **closed-reference**, **open-reference** and **swarm** OTU picking protocols;
        * **state-of-the-art taxonomic classification** algorithms are
          available (RDP and consensus-based classifier);
        * fast (multithread) and and memory efficient implementation of the
          **NAST** multiple sequence alignment (MSA);
        * filters low quality sequences according to the maximum allowed **expected
          error (EE) rate** %;
        * runs on **Linux**, **Mac OS X** and **MS Windows** (through Docker
          containers)
        * **simple, easy to use**.
        
        
        Docker images
        -------------
        Docker images are available (compmetagen/micca) starting from version 1.2.2,
        see the documentation (>=1.3.0) to learn how to use them. `Docker hub page:
        <https://hub.docker.com/r/compmetagen/micca/>`_.
        
        
        Citing micca
        ------------
        
        Davide Albanese, Paolo Fontana, Carlotta De Filippo, Duccio Cavalieri
        and Claudio Donati. **MICCA: a complete and accurate software for
        taxonomic profiling of metagenomic data**. Scientific Reports 5,
        Article number: 9743 (2015), doi:10.1038/srep09743, `Link
        <http://www.nature.com/articles/srep09743/>`_. `Dataset download
        <ftp://ftp.fmach.it/metagenomics/micca/scirep/>`_.
        
        micca wraps third party software packages and these **should be
        cited** if they are used:
        
        * VSEARCH (https://github.com/torognes/vsearch) used in ``classify``,
          ``filter``, ``mergepairs``, ``otu`` and ``msa`` commands
        * MUSCLE (doi: 10.1093/nar/gkh340) used in ``msa`` and ``tree`` commands
        * FastTree (doi: 10.1371/journal.pone.0009490) used in the ``tree`` command
        * Cutadapt (doi: 10.14806/ej.17.1.200) used in the ``trim`` command
        * RDP classifier (doi:10.1128/AEM.00062-07) used in the ``classify`` command
        * swarm (10.7717/peerj.593, doi: 10.7717/peerj.1420) used in the ``otu`` command
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: C
Classifier: Programming Language :: C++
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Environment :: Console
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
