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    "info": {
        "author": "Wouter De Coster",
        "author_email": "decosterwouter@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# NanoComp\n\n\nCompare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.\n\nAs of version 1.1.0 NanoComp will also create a static png image for dynamic html plots, as the latter can get quite big and slow to load for big datasets. This however requires that you install [orca](https://github.com/plotly/orca). Without orca the script still works, but no static copies of dynamic plots are created.\n\n[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)\n[![Build Status](https://travis-ci.org/wdecoster/nanocomp.svg?branch=master)](https://travis-ci.org/wdecoster/nanocomp)\n\n### INSTALLATION\n`pip install NanoComp`  \n\nThis script is written for Python3.\n\n### USAGE\n```\nNanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]\n                [--raw] [--readtype {1D,2D,1D2}] [--barcoded]\n                [--split_runs TSV_FILE]\n                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]\n                [-n names [names ...]] [--plot {violin,box}] [--title TITLE]\n                (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])\n\nGeneral options:\n  -h, --help            show the help and exit\n  -v, --version         Print version and exit.\n  -t, --threads THREADS\n                        Set the allowed number of threads to be used by the script\n  -o, --outdir OUTDIR   Specify directory in which output has to be created.\n  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.\n  --verbose             Write log messages also to terminal.\n  --raw                 Store the extracted data in tab separated file.\n\nOptions for filtering or transforming input prior to plotting:\n  --readtype {1D,2D,1D2}\n                        Which read type to extract information about from summary. Options are 1D, 2D,\n                        1D2\n  --barcoded            Barcoded experiment in summary format, splitting per barcode.\n  --split_runs TSV_FILE\n                        File: Split the summary on run IDs and use names in tsv file. Mandatory header\n                        fields are 'NAME' and 'RUN_ID'.\n\nOptions for customizing the plots created:\n  -f, --format {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}\n                        Specify the output format of the plots.\n  -n, --names names     Specify the names to be used for the datasets\n  -c, --colors colors   Specify the colors to be used for the datasets\n  --plot {violin,box,ridge,false}\n                        Which plot type to use: 'box', 'violin' (default), 'ridge' (joyplot) or 'false' (no plots)\n  --title TITLE         Add a title to all plots, requires quoting if using spaces\n\nInput data sources, one of these is required.:\n  --fastq files [files ...]\n                        Data is in (compressed) fastq format.\n  --fasta files [files ...]\n                        Data is in (compressed) fasta format.\n  --summary files [files ...]\n                        Data is in (compressed) summary files generated by albacore or guppy.\n  --bam files [files ...]\n                        Data is in sorted bam files.\n\n```\n\n[Example file for --split_runs](https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv)\n\n\n\n\n\n\n### EXAMPLES\n```\nNanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs\nNanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4\n```\n\n\n### EXAMPLE OUTPUT\n![loglength example](https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png)\n![box percentIdentity example](https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png)\n\n[See more examples](https://github.com/wdecoster/nanocomp/tree/master/examples)\n\nI welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanocomp/issues) or open a pull request. I will usually respond within a day, or rarely within a few days.\n\n\n## CITATION\nIf you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).",
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