Metadata-Version: 2.1
Name: nanoQC
Version: 0.9.4
Summary: Create fastQC-like plots for Oxford Nanopore sequencing data
Home-page: https://github.com/wdecoster/nanoQC
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: GPLv3
Description: # nanoQC
        Quality control tools for long read sequencing data aiming to replicate some of the plots made by fastQC. This is an immature tool and I welcome all contributions.
        
        [![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/nanoqc/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoqc)
        
        
        Creates dynamic plots using [bokeh](https://bokeh.pydata.org/en/latest/).
        For an example see [here](http://decoster.xyz/wouter/)
        
        
        ## INSTALLATION
        ```bash
        pip install nanoQC
        ```
        or  
        [![install with conda](https://anaconda.org/bioconda/nanoqc/badges/installer/conda.svg)](https://anaconda.org/bioconda/nanoqc)
        ```
        conda install -c bioconda nanoqc
        ```
        
        
        ## USAGE
        ```
        nanoQC [-h] [-v] [-o OUTDIR] fastq
        
        positional arguments:
          fastq                 Reads data in fastq.gz format.
        
        optional arguments:
          -h, --help            show this help message and exit
          -v, --version         Print version and exit.
          -o, --outdir OUTDIR   Specify directory in which output has to be created.
          -l, --minlen int      Minimum length of reads to be included in the plots
                                This also controls the length plotted in the graphs
                                from the beginning and end of reads (length plotted = minlen / 2)
        ```
        
        ## CITATION
        If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
        
        ## CONTRIBUTIONS
        Thanks to:
         -  Jasper Ouwerkerk ([JasperO98](https://github.com/JasperO98)) for improving how reads are selected (v0.8.0)
        
Keywords: nanopore sequencing statistics
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
Requires-Python: >=3
Description-Content-Type: text/markdown
