Metadata-Version: 2.1
Name: metator
Version: 0.1.7
Summary: A pipeline for binning metagenomic datasets from 3C data.
Home-page: https://github.com/koszullab/metator
Author: lyam.baudry@pasteur.fr
License: GPLv3
Description: # metaTOR
        
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        Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamline the processing and binning of metagenomic 3C datasets.
        
        ## Installation
        
        ```sh
           pip3 install metator
        ```
        
        or, to use the latest version:
        
        ```sh
           pip3 install -e git+https://github.com/koszullab/metator.git@master#egg=metator
        ```
        
        Python 3.4 or later is required. A [standalone version](https://github.com/koszullab/metaTOR/tree/python3-standalone) (no installation, just download/unzip/run) is also available, as well as a [Python 2 version](https://github.com/koszullab/metaTOR/tree/python2), but keep in mind that development will focus on the current branch.
        
        ## Usage
        
            metator {align|partition|annotation|binning} [parameters]
        
        A metaTOR command takes the form ```metator action --param1 arg1 --param2
        arg2 #etc.```
        
        There are four actions/steps in the metaTOR pipeline, which must be run in the following order:
        
        * ```align``` : map paired-end reads on a preliminary assembly, then generate a network from
         detected contacts between DNA chunks.
        
        * ```partition``` : perform the Louvain community detection algorithm many times to isolate
             chunks that consistently cluster together for binning purposes.
        
        * ```annotation``` : run standard annotation software on the assembly (namely gene prediction
              and database comparison) to match with the bins.
        
        * ```binning``` : match annotations to bins, extract bin genomes and subnetworks, build bin-local
           and global contact maps.
        
        After the last step is completed there should be a set of bins, their relative enrichments in various gene categories, and the contact map of each bin.
        
        There are a number of other, optional, miscellaneous actions:
        
        * ```pipeline``` : check the environment is right, then run all four of the above actions sequentially.
            This can take a while.
        
        * ```dependencies``` : download third party dependencies that are not available in most package managers.
        
        * ```deploy``` : set up the environment and all dependencies for Ubuntu 14.04 and higher (run as root).
        
        * ```version``` : display current version number.
        
        * ```help``` : display this help message.
        
        Please refer to the [tutorial](https://github.com/koszullab/metaTOR/blob/master/doc/TUTORIAL.md) in order to quickly get the pipeline up and running on example data (or your own), and the [metaTOR manual](https://github.com/koszullab/metaTOR/blob/master/metator_manual.pdf) for detailed explanations on the parameters.
        
        ## Requirements
        
        * Python 3 with ```numpy```, ```scipy```, ```matplotlib```, ```biopython``` and ```pysam``` libraries.
        * [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
        * [samtools](http://www.htslib.org/)
        * [hmmer](http://hmmer.org/) and some HMM databases (such as [these](http://dl.pasteur.fr/fop/LItxiFe9/hmm_databases.tgz))
        * [prodigal](https://github.com/hyattpd/Prodigal)
        * [louvain](https://sourceforge.net/projects/louvain/) (original
            implementation)
        
        Requirements can usually be installed with an OS's package manager. The requirements that cannot (namely ```prodigal```, ```louvain``` and HMM databases) can be fetched with the following (The package may need to be run as a root depending on where the package is installed):
        
        ```sh
            metator dependencies
        ```
        
        ## Containers
        
        A dockerfile is also available if that is of interest. You may fetch the image by running the following:
        
        ```sh
            docker pull koszullab/metator
        ```
        
        Additionally, a [Singularity](https://www.sylabs.io/) file is also available, courtesy of [avilab](https://github.com/avilab/metator). You may fetch the container this way:
        
        ```sh
            singularity pull shub://kosullab/metator
        ```
        
        ## References
        
        * [Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381813/), Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, and Romain Koszul, eLife, 2014
        * [Meta3C analysis of a mouse gut microbiome](https://www.biorxiv.org/content/early/2015/12/17/034793), Martial Marbouty, Lyam Baudry, Axel Cournac, Romain Koszul, 2015
        * [Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315449/), Martial Marbouty, Lyam Baudry, Axel Cournac, and Romain Koszul, Science Advances, 2017
        
        ## Contact
        
        ### Authors
        
        * lyam.baudry@pasteur.fr
        * thfoutel@pasteur.fr
        * martial.marbouty@pasteur.fr
        * romain.koszul@pasteur.fr
        
        ### Research lab
        
        [Spatial Regulation of Genomes](https://research.pasteur.fr/en/team/spatial-regulation-of-genomes/) (Institut Pasteur, Paris)
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
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