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        "author": "Wouter De Coster",
        "author_email": "decosterwouter@gmail.com",
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            "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"
        ],
        "description": "# NanoLyse\nRemove reads mapping to the lambda phage genome from a fastq file.  \nThis script uses Heng Li's [minimap2](https://github.com/lh3/minimap2) and his [mappy](https://pypi.python.org/pypi/mappy) Python binding.\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/nanolyse.svg?branch=master)](https://travis-ci.org/wdecoster/nanolyse) [![Code Health](https://landscape.io/github/wdecoster/nanolyse/master/landscape.svg?style=flat)](https://landscape.io/github/wdecoster/nanolyse/master)\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/nanolyse/README.html)\n\n\n### INSTALLATION\n`pip install NanoLyse`\n\n### USAGE\n```\nReads fastq from stdin and writes to stdout.  \n\nNanoLyse [-h] [-v] [-r REFERENCE]\n\n                    Remove reads mapping to the lambda genome.\n                    Reads fastq from stdin and writes to stdout.\n\n                    Example usage:\n                    zcat reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz\n\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --version         Print version and exit.\n  -r REFERENCE, --reference REFERENCE\n                        Specify a reference fasta file against which to filter.\n```\n\n\n### WARNING\nIf (some of) the reads of your genome of interest are sufficiently similar to the lambda genome those reads will be lost.\n\n### EXAMPLES\n`gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz`  \nIn combination with [NanoFilt](https://github.com/wdecoster/nanofilt):  \n`gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz`  \nUsing a different genome to filter on (rather than lambda phage):  \n`gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz`  \n\n\n\n\n\n\n\n\n\nI welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanolyse/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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