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        "description": "# nanoget\nThis module provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments.  \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[![install with conda](https://anaconda.org/bioconda/nanoget/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoget)\n[![Build Status](https://travis-ci.org/wdecoster/nanoget.svg?branch=master)](https://travis-ci.org/wdecoster/nanoget)\n\n\n## FUNCTIONS\nData can be presented in the following formats, using the following functions:  \n- A sorted bam file `process_bam(bamfile, threads)`  \n- A standard fastq file `process_fastq_plain(fastqfile, 'threads')`  \n- A fastq file with metadata from MinKNOW or Albacore `process_fastq_rich(fastqfile)`  \n- A sequencing_summary file generated by Albacore `process_summary(sequencing_summary.txt, 'readtype')`  \n\nFastq files can be compressed using gzip, bzip2 or bgzip. The data is returned as a pandas DataFrame with standardized headernames for convenient extraction. The functions perform logging while being called and extracting data.\n\n\n## INSTALLATION\n```bash\npip install nanoget\n```\nor  \n[![install with conda](https://anaconda.org/bioconda/nanoget/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoget)\n```\nconda install -c bioconda nanoget\n```\n\nCopyright: 2016-2020 Wouter De Coster <decosterwouter@gmail.com>",
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