Metadata-Version: 1.1
Name: NanoPlot
Version: 0.18.0
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: 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 but also seems to work for python2.7.
        
        USAGE
        ~~~~~
        
        ::
        
        
            NanoPlot [-h] [-v] [-t THREADS] [--maxlength MAXLENGTH]
                    [--drop_outliers] [--downsample DOWNSAMPLE] [--loglength]
                    [--alength] [-o OUTDIR] [-p PREFIX]
                    (--fastq FASTQ | --fastq_rich FASTQ_RICH | --summary SUMMARY | --bam BAM)
        
        
            Required input argument is (exact) one of these:
                --fastq FASTQ           Data presented is in fastq format exported from fast5
                                        files by e.g. poretools.
                --fastq_rich FASTQ_rich Data presented is in fastq format generated by
                                        Albacore or MinKNOW with additional information concerning
                                        channel and time.
                --bam BAM               Data presented as a sorted bam file.
                --summary SUMMARY       Data is a summary file generated by albacore.
            Each of these options can take one or multiple files e.g.
            --summary summary1.txt summary2.txt summary3.txt
            --bam bam1.txt bam2.txt
        
        
            Arguments for optional filtering:
                --readtype              Specify read type to extract from summary file
                                        Options: 1D (default), 2D or 1D2
                --maxlength MAXLENGTH   Drop reads longer than length N.
                --downsample DOWNSAMPLE Reduce dataset to N reads by random sampling.
                --drop_outliers         Drop outlier reads with extreme long length.
                --loglength             Logarithmic scaling of lengths in plots.
                --alength               Use aligned read lengths rather than sequenced length (bam mode).
        
        
            Optional output arguments:
                -o, --outdir OUTDIR     Specify directory in which output has to be created.
                -p, --prefix PREFIX     Specify a prefix to be used for the output files.
                -c, --color COLOR       Specify a color for the plots
                                        must be a valid matplotlib color (see color_options.txt)
                                        default: green
                -f, --format FORMAT     Specify the output format for the plots,
                                        options are: eps, jpg, pdf, png, ps, svg
                                        default: png
                --plots PLOTS           Specify which type of bivariate plots have to be made
                                        options are: hex, kde, dot (multiple can be specified together)
                                        default: all
        
        
            General arguments:
                -h, --help              show this help message and exit
                -v, --version           Print version and exit.
                -t, --threads THREADS   Max number of threads to be used by the script
                --listcolors            Give a list of all colors which can be used for plotting
        
        `ACKNOWLEDGMENTS <https://github.com/wdecoster/NanoPlot/blob/master/ACKNOWLEDGMENTS.MD>`__
        ------------------------------------------------------------------------------------------
        
        COMPANION SCRIPTS
        -----------------
        
        -  `NanoFilt <https://github.com/wdecoster/nanofilt>`__: filtering and
           trimming of reads
        -  `NanoStat <https://github.com/wdecoster/nanostat>`__: statistic
           summary report of reads or alignments
        
        .. |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
