Metadata-Version: 1.1
Name: NanoStat
Version: 0.3.0
Summary: Calculate statistics for Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/nanostat
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description: NanoStat
        ========
        
        Calculate various statistics from an Oxford Nanopore dataset in fastq,
        bam or albacore sequencing summary format.
        
        |Twitter URL| |install with conda| |Build Status| |Code Health|
        
        INSTALLATION
        ~~~~~~~~~~~~
        
        .. code:: bash
        
            pip install nanostat
        
        | or
        | |install with conda|
        
        ::
        
            conda install -c bioconda nanostat
        
        USAGE
        ~~~~~
        
        ::
        
            NanoStat [-h] [-v] [-o OUTDIR] [-p PREFIX] [-t THREADS]
                            (--fastq FASTQ | --summary SUMMARY | --bam BAM)
        
            Get statistics of Oxford Nanopore read dataset.
        
            Mandatory one of the following data sources:
            --fastq FASTQ         Data is in fastq format.
            --summary SUMMARY     Data is a summary file generated by albacore.
            --bam BAM             Data as a sorted bam file.
        
        
            Optional arguments:
              --readtype              Specify read type to extract from summary file
                                    Options: 1D (default), 2D or 1D2
              -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.
              -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
              -t, --threads THREADS Set the allowed number of threads to be used by the script
                                    This only applies to bam and fastq format as data source
        
        STATUS
        ------
        
        |Build Status| |Code Health|
        
        Example output
        ~~~~~~~~~~~~~~
        
        ::
        
            Number of reads:    408254
            Total bases:    3508315665
            Median read length: 5168.0
            Mean read length:   8593.46
            Readlength N50: 39346
        
            Top 5 read lengths and their average basecall quality score:
            Length: 255821bp    Q: 6.84
            Length: 254573bp    Q: 7.09
            Length: 253711bp    Q: 6.96
            Length: 245784bp    Q: 6.98
            Length: 245776bp    Q: 7.06
        
            Top 5 average basecall quality scores and their read lengths:
            Length: 407bp   Q: 16.22
            Length: 880bp   Q: 16.18
            Length: 729bp   Q: 16.12
            Length: 1057bp  Q: 16.08
            Length: 841bp   Q: 15.84
        
            Number of reads and fraction above quality cutoffs:
            Q5: 406428  99.55%
            Q10:    305509  74.83%
            Q15:    124 0.03%
            Q20:    0   0.0%
        
        .. |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/nanostat/badges/installer/conda.svg
           :target: https://anaconda.org/bioconda/nanostat
        .. |Build Status| image:: https://travis-ci.org/wdecoster/nanostat.svg?branch=master
           :target: https://travis-ci.org/wdecoster/nanostat
        .. |Code Health| image:: https://landscape.io/github/wdecoster/nanostat/master/landscape.svg?style=flat
           :target: https://landscape.io/github/wdecoster/nanostat/master
        
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
