Metadata-Version: 1.1
Name: NanoPlot
Version: 0.26.0
Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoPlot
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: NanoPlot
        ========
        
        Plotting tool for Oxford Nanopore sequencing data and alignments.
        
        |Twitter URL| |conda badge| |Build Status| |Code Health|
        
        .. figure:: https://github.com/wdecoster/NanoPlot/blob/master/examples/scaled_Log_Downsampled_LengthvsQualityScatterPlot_kde.png
           :alt: Example plot
        
           Example plot
        
        The example plot above shows a bivariate plot comparing log transformed
        read length with average basecall Phred quality score. More examples can
        be found in the `gallery on my blog 'Gigabase Or
        Gigabyte'. <https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/>`__
        
        In addition to various plots also a NanoStats file is created
        summarizing key features of the dataset.
        
        | This script performs data extraction from Oxford Nanopore sequencing
          data in the following formats:
        | - fastq files
        | (can be bgzip, bzip2 or gzip compressed)
        | - fastq files generated by albacore or MinKNOW containing additional
          information
        | (can be bgzip, bzip2 or gzip compressed)
        | - sorted bam files
        | - sequencing\_summary.txt output table generated by albacore
        
        INSTALLATION
        ~~~~~~~~~~~~
        
        ``pip install NanoPlot``
        
        | Upgrade to a newer version using:
        | ``pip install NanoPlot --upgrade``
        
        or
        
        | |conda badge|
        | ``conda install -c bioconda nanoplot``
        
        STATUS
        ~~~~~~
        
        |Build Status| |Code Health|
        
        The script is written for python3.
        
        USAGE
        ~~~~~
        
        \`\`\` NanoPlot [-h] [-v] [-t THREADS] [--verbose] [-o OUTDIR] [-p
        PREFIX] [--maxlength N] [--drop\_outliers] [--downsample N][--loglength]
        [--alength] [--minqual N] [--readtype {1D,2D,1D2}] [--barcoded] [-c
        COLOR][-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
        [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre}
        ...]]][--listcolors] (--fastq file [file ...] \| --fastq\_rich file
        [file ...] \| --fastq\_minimal file [file ...] \| --summary file [file
        ...] \| --bam file [file ...])
        
        General options: -h, --help show the help and exit -v, --version Print
        version and exit. -t, --threads THREADS Set the allowed number of
        threads to be used by the script --verbose Write log messages also to
        terminal. -o, --outdir OUTDIR Specify directory in which output has to
        be created. -p, --prefix PREFIX Specify an optional prefix to be used
        for the output files.
        
        Input data sources, one of these is required.: --fastq file [file ...]
        Data is in one or more default fastq file(s). --fastq\_rich file [file
        ...] Data is in one or more fastq file(s) generated by albacore or
        MinKNOW with additional information concerning channel and time.
        --fastq\_minimal file [file ...] Data is in one or more fastq file(s)
        generated by albacore or MinKNOW with additional information concerning
        channel and time. Minimal data is extracted swiftly without elaborate
        checks. --summary file [file ...] Data is in one or more summary file(s)
        generated by albacore. --bam file [file ...] Data is in one or more
        sorted bam file(s).
        
        Each of these options can take one or multiple files e.g. --summary
        summary1.txt summary2.txt summary3.txt --bam bam1.txt bam2.txt
        
        Options for filtering or transforming input prior to plotting:
        --maxlength N Drop reads longer than length specified. --drop\_outliers
        Drop outlier reads with extreme long length. --downsample N Reduce
        dataset to N reads by random sampling. --loglength Logarithmic scaling
        of lengths in plots. --alength Use aligned read lengths rather than
        sequenced length (bam mode) --minqual N Drop reads with an average
        quality lower than specified. --readtype {1D,2D,1D2} Which read type to
        extract information about from summary. Options are 1D, 2D, 1D2
        --barcoded Use if you want to split the summary file by barcode
        
        Options for customizing the plots created: -c, --color COLOR Specify a
        color for the plots, must be a valid matplotlib color -f, --format
        {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff} Specify the
        output format of the plots. --plots [{kde,hex,dot,pauvre}
        [{kde,hex,dot,pauvre} ...]] Specify which bivariate plots have to be
        made. --listcolors List the colors which are available for plotting and
        exit.\`\`\`
        
        EXAMPLES
        ~~~~~~~~
        
        ``bash Nanoplot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed   NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled``
        
        This script now also provides read length vs mean quality plots in the
        '`pauvre <https://github.com/conchoecia/pauvre>`__'-style from
        [@conchoecia](https://github.com/conchoecia).
        
        `ACKNOWLEDGMENTS <https://github.com/wdecoster/NanoPlot/blob/master/ACKNOWLEDGMENTS.MD>`__
        ------------------------------------------------------------------------------------------
        
        I welcome all suggestions, bug reports, feature requests and
        contributions. Please leave an
        `issue <https://github.com/wdecoster/NanoPlot/issues>`__ or open a pull
        request. I will usually respond within a day, or rarely within a few
        days.
        
        COMPANION SCRIPTS
        -----------------
        
        -  `NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing
           multiple runs
        -  `NanoStat <https://github.com/wdecoster/nanostat>`__: statistic
           summary report of reads or alignments
        -  `NanoFilt <https://github.com/wdecoster/nanofilt>`__: filtering and
           trimming of reads
        -  `NanoLyse <https://github.com/wdecoster/nanolyse>`__: removing
           contaminant reads (e.g. lambda control DNA) from fastq
        
        .. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
           :target: https://twitter.com/wouter_decoster
        .. |conda badge| image:: https://anaconda.org/bioconda/nanoplot/badges/installer/conda.svg
           :target: https://anaconda.org/bioconda/nanoplot
        .. |Build Status| image:: https://travis-ci.org/wdecoster/NanoPlot.svg?branch=master
           :target: https://travis-ci.org/wdecoster/NanoPlot
        .. |Code Health| image:: https://landscape.io/github/wdecoster/NanoPlot/master/landscape.svg?style=flat
           :target: https://landscape.io/github/wdecoster/NanoPlot/master
        
Keywords: nanopore sequencing plotting quality control
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
