Metadata-Version: 1.1
Name: multiqc
Version: 0.2.0
Summary: Create aggregate bioinformatics analysis report across many samples
Home-page: https://github.com/ewels/MultiQC
Author: Phil Ewels
Author-email: phil.ewels@scilifelab.se
License: MIT
Download-URL: https://github.com/ewels/MultiQC/releases
Description: # [<img src="multiqc/templates/default/assets/img/MultiQC_logo.png" width="300" title="MultiQC">](https://github.com/ewels/MultiQC)
        
        **MultiQC is a tool to aggregate bioinformatics results across many samples into
        a single report.**
        
        [![Build Status](https://travis-ci.org/ewels/MultiQC.svg?branch=master)](https://travis-ci.org/ewels/MultiQC)
        
        It is written in Python and contains modules for a number of common tools.
        Currently, these include:
        
        * [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
        * [FastQ Screen](http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)
        * [Cutadapt](https://code.google.com/p/cutadapt/)
        * [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/)
        * [STAR](https://github.com/alexdobin/STAR)
        * [Tophat](https://ccb.jhu.edu/software/tophat/)
        * [Bowtie](http://bowtie-bio.sourceforge.net)
        * [Bowtie 2](http://bowtie-bio.sourceforge.net/bowtie2/)
        * [Subread featureCounts](http://bioinf.wehi.edu.au/featureCounts/)
        * [Picard MarkDuplicates](http://broadinstitute.github.io/picard/)
        
        More to come soon. Please suggest any ideas as a new
        [issue](https://github.com/ewels/MultiQC/issues).
        
        ## Graphical Usage
        
        MultiQC comes with a graphical app for OS X. To use, download `MultiQC.app.zip`
        from the [releases page](https://github.com/ewels/MultiQC/releases)
        and unzip the archive. Double click MultiQC.app to launch, then
        drag your analysis directory onto the window.
        
        The app can be run from anywhere, though we recommend copying to your
        Applications directory.
        
        A similar graphical utility for Windows is planned for a future release.
        
        ## Command Line Usage
        
        You can install MultiQC from [PyPI](https://pypi.python.org/pypi/multiqc/0.1)
        using `pip` as follows:
        
        ```
        pip install multiqc
        ```
        
        If you would like the development version instead, the command is:
        
        ```
        pip install git+https://github.com/ewels/MultiQC.git
        ```
        
        Then it's just a case of going to your analysis directory and running the script:
        
        ```
        multiqc .
        ```
        
        That's it! MultiQC will scan the specified directory ('.' is the current dir)
        and produce a report detailing whatever it finds.
        
        The report is created in `multiqc_report/multiqc_report.html` by default.
        A zip file of the report is also generated to facilitate easy transfer and sharing.
        
        Tab-delimited data files are also created in `multiqc_report/report_data/`,
        containing extra information. These can be easily inspected using Excel.
        
        For more detailed instructions, run `multiqc -h`
        
        ## Contributions & Support
        
        Contributions and suggestions for new features are welcome, as are bug reports!
        Please create a new [issue](https://github.com/ewels/MultiQC/issues) for any
        of these, including example reports where possible.
        
        Pull requests with new code are always gladly received, see the
        [contributing notes](https://github.com/ewels/MultiQC/blob/master/CONTRIBUTING.md)
        for details. These notes include extensive help with how to use the built in code.
        
        If in doubt, feel free to get in touch with the author:
        [@ewels](https://github.com/ewels) (phil.ewels@scilifelab.se)
        
        ## Version History
        #### v0.2 - 2015-09-18
        * Code restructuring for nearly all modules. Common base module
          functions now handle many more functions (plots, config, file import)
          * See the [contributing notes](https://github.com/ewels/MultiQC/blob/master/CONTRIBUTING.md)
            for instructions on how to use these new helpers to make your own module
        * New report toolbox - sample highlighting, renaming, hiding
          * Config is autosaved by default, can also export to a file for sharing
          * Interactive tour to help users find their way around
        * New Tophat, Bowtie 2 and QualiMap modules
          * Thanks to @guillermo-carrasco for the QualiMap module
        * Bowtie module now works
        * New command line parameter `-d` prefixes sample names with the directory that
          they were found in. Allows duplicate filenames without being overwritten.
        * Introduction walkthrough helps show what can be done in the report
        * Now compatible with both Python 2 and Python 3
        * Software version number now printed on command line properly, and in reports.
        * Bugfix: FastQC doesn't break when only one report found
        * Bugfix: FastQC seq content heatmap highlighting
        * Many, many small bugfixes
        
        #### [v0.1](https://github.com/ewels/MultiQC/releases/tag/v0.1) - 2015-09-01
        * The first public release of MultiQC, after a month of development. Basic
        structure in place and modules for FastQC, FastQ Screen, Cutadapt, Bismark, 
        STAR, Bowtie, Subread featureCounts and Picard MarkDuplicates. Approaching
        stability, though still under fairly heavy development.
        
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Programming Language :: JavaScript
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
