Metadata-Version: 1.1
Name: NanoStat
Version: 0.8.0
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-Content-Type: UNKNOWN
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
        ~~~~~~~~~~~~
        
        | ``pip install nanostat``
        | or
        | ``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.
            Specifying a list of files of the same type is supported.
        
            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.
              -n, --name NAME       Specify a custom filename/path for the output,
                                    <stdout> for printing to stdout.
              -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
        
        EXAMPLES
        ^^^^^^^^
        
        ::
        
            NanoStat --fastq reads.fastq.gz --outdir statreports
            NanoStat --summary sequencing_summary1.txt sequencing_summary2.txt sequencing_summary3.txt --readtype 1D2
            NanoStat --bam alignment.bam alignment2.bam```
        
            ### Example output
        
        Number of reads: 99875 Total bases: 779100562 Median read length: 5456.0
        Mean read length: 7800.76 Readlength N50: 12658
        
        Top 5 read lengths and their average basecall quality score: Length:
        299625bp Q: 10.36 Length: 272879bp Q: 9.99 Length: 271441bp Q: 10.94
        Length: 261038bp Q: 8.0 Length: 250267bp Q: 7.74
        
        Top 5 average basecall quality scores and their read lengths: Length:
        1455bp Q: 16.54 Length: 3634bp Q: 16.48 Length: 733bp Q: 16.23 Length:
        515bp Q: 16.2 Length: 909bp Q: 15.89
        
        Number of reads and fraction above quality cutoffs: Q5: 88489 88.6% Q10:
        61809 61.89% Q15: 175 0.18% Q20: 0 0.0%
        
        Data produced using 512 active channels.
        
        Data was produced in run(s) with ID:
        002dc25e406b22dd8e4d2a5ee83dcbb67072e10d
        005aaa922c42c455c07a472a9c30f0209f1b0d93
        00b31b64541f79ff1f562c3e3602d3f265cd3b05
        00c9faabd00f4676a2255da178a62c1fe6ae061b
        00f9dec9cb591f4cb4c60c129f87faf731323386 \`\`\`
        
        I welcome all suggestions, bug reports, feature requests and
        contributions. Please leave an
        `issue <https://github.com/wdecoster/nanostat/issues>`__ or open a pull
        request. I will usually respond within a day, or rarely within a few
        days.
        
        .. |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
