Metadata-Version: 1.1
Name: nanoget
Version: 0.19.3
Summary: Functions to extract information from Oxford Nanopore sequencing data and alignments.
Home-page: https://github.com/wdecoster/nanoget
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: nanoget
        =======
        
        This module provides functions to extract useful metrics from Oxford
        Nanopore sequencing reads and alignments.
        
        |Twitter URL| |install with conda| |Build Status| |Code Health|
        
        FUNCTIONS
        ---------
        
        | Data can be presented in the following formats, using the following
          functions:
        | - A sorted bam file ``process_bam(bamfile, threads)``
        | - A standard fastq file ``process_fastq_plain(fastqfile, 'threads')``
        | - A fastq file with metadata from MinKNOW or Albacore
          ``process_fastq_rich(fastqfile)``
        | - A sequencing\_summary file generated by Albacore
          ``process_summary(sequencing_summary.txt, 'readtype')``
        
        Fastq 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.
        
        INSTALLATION
        ------------
        
        .. code:: bash
        
            pip install nanoget
        
        | or
        | |install with conda|
        
        ::
        
            conda install -c bioconda nanoget
        
        STATUS
        ------
        
        |Build Status| |Code Health|
        
        .. |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
        .. |install with conda| image:: https://anaconda.org/bioconda/nanoget/badges/installer/conda.svg
           :target: https://anaconda.org/bioconda/nanoget
        .. |Build Status| image:: https://travis-ci.org/wdecoster/nanoget.svg?branch=master
           :target: https://travis-ci.org/wdecoster/nanoget
        .. |Code Health| image:: https://landscape.io/github/wdecoster/nanoget/master/landscape.svg?style=flat
           :target: https://landscape.io/github/wdecoster/nanoget/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
