Metadata-Version: 2.1
Name: nanoget
Version: 1.15.0
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: GPLv3
Description: # nanoget
        This module provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments.  
        
        [![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)
        [![install with conda](https://anaconda.org/bioconda/nanoget/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoget)
        [![Build Status](https://travis-ci.org/wdecoster/nanoget.svg?branch=master)](https://travis-ci.org/wdecoster/nanoget)
        
        
        ## 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
        ```bash
        pip install nanoget
        ```
        or  
        [![install with conda](https://anaconda.org/bioconda/nanoget/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoget)
        ```
        conda install -c bioconda nanoget
        ```
        
        Copyright: 2016-2020 Wouter De Coster <decosterwouter@gmail.com>
        
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 :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Python: >=3
Description-Content-Type: text/markdown
