Metadata-Version: 1.1
Name: NanoStat
Version: 0.2.1
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 format as data source, the rest uses one thread by default
        
        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
