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    "info": {
        "author": "Christopher Rushton",
        "author_email": "ckrushto@sfu.ca",
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        "classifiers": [
            "License :: OSI Approved :: GNU Affero General Public License v3",
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            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "[![Build Status](https://travis-ci.org/morinlab/Dellingr.svg?branch=master)](https://travis-ci.org/morinlab/Dellingr)\n\n# Dellingr\nAn error supression and variant calling pipeline for Second-Generation sequencing data\n\n## Description\n\nSee the full wiki page for more information: http://produse.readthedocs.io/en/latest/\n\n## Installation \n\n### Dependencies\n\nYou will need to install the following before installing Dellingr:\n\n* `3.7>python>=3.4`\n* `bwa>=0.7.0`\n* `samtools>=1.3.1`\n\nDellingr will check these dependencies prior to running the pipeline\n\nTo install the Dellingr package run the following command:\n\n### Install using the Python Package Index (PyPI)\n```bash\npip install Dellingr\n```\n\n### Install from Github\n```bash\ngit clone https://github.com/morinlab/Dellingr.git\ncd Dellingr\npython setup.py install\n```\nAll required python dependencies will be installed during this step\n\n## Running Dellingr\n\n### The Analysis Pipeline: Very Quick Start\n\nYou can view more detailed instructions on the [wiki](http://produse.readthedocs.io/en/latest/)\n\nAll parameters required to run ProDuSe can be viewed using the following:\n```bash\n    dellingr run_dellingr -h\n```\n\nAlternatively, if you wish to run Dellingr without installing it, you can run `DellingrPipeline.py` manually in a similar manner:\n```bash\n    /path/to/Dellingr/DellingrPipeline.py -h\n```\n\nWhile these parameters can be specified individually, they can also be provided using a configuration file\n\nTo run the analysis pipeline you simply need to run the following command:\n```bash\n    dellingr run_dellingr\n    -c /path/to/github/clone/etc/dellingr_config.ini\n```\n\nAlternatively:\n```bash\n    /path/to/Dellingr/DellingrPipeline.py \n    -c /path/to/github/clone/etc/dellingr_config.ini\n```\n\nThis will run the entire Dellingr pipeline on all samples specified in the sample_config.ini file, which can be found in \netc/sample_config.ini\n\nResults will be located in the following directory:\n\n```bash\nls ./dellingr_analysis_directory\n```\n\n### Helper Scripts\n\nThe Dellingr package is comprised of several stages to aid in the analysis of duplex sequencing data.\n\nThese stages can be be viewed by running the following:\n\n```bash\ndellingr -h\n```\n\n#### dellingr adapter_predict\n\nIf you need to confirm the expected adapter sequence of a sample you should run the following command:\n\n```bash\ndellingr adapter_predict -i input1.fastq input2.fastq\n```\n\nThis tool will print a predicted adapter sequence based off of ACGT abundances at each position. It uses these observed abundances and finds the closest expected abundance for an IUPAC unambiguous or ambiguous base.",
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