Metadata-Version: 1.2
Name: nanopack
Version: 1.1.0
Summary: Install all Oxford Nanopore scrips and modules for processing and analysis
Home-page: https://github.com/wdecoster/nanopack
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: GPLv3
Description: NANOPACK
        ========
        
        Easily install all my long read processing and analysis scripts
        simultaneously.
        
        Installation
        ------------
        
        ``pip install nanopack`` ## Updating ``pip install nanopack --upgrade``
        
        These scripts are written and tested for Python3, and may not work on
        Python2.
        
        Content
        -------
        
        Scripts
        ~~~~~~~
        
        `NanoPlot <https://github.com/wdecoster/NanoPlot>`__: creating many
        relevant plots derived from reads (fastq), alignments (bam) and albacore
        summary files. Examples can be found in `the gallery on my
        blog <https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/>`__.
        NanoPack is also available with a graphical user interface in
        `NanoGUI <https://github.com/wdecoster/nanogui>`__ or as a `web
        service <http://nanoplot.bioinf.be>`__.
        
        `NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing multiple
        runs on read length and quality based on reads (fastq), alignments (bam)
        or albacore summary files.
        
        `NanoQC <https://github.com/wdecoster/nanoQC>`__: Generating plots to
        investigate nucleotide composition and quality distribution at the end
        of reads.
        
        `NanoStat <https://github.com/wdecoster/nanostat>`__: Quickly create a
        statistical summary from reads, an alignment or a summary file.
        
        `NanoFilt <https://github.com/wdecoster/nanofilt>`__: Streaming script
        for filtering a fastq file based on a minimum length, minimum quality
        cut-off, minimum and maximum average GC. Also trimming nucleotides from
        either read ends is an option.
        
        `NanoLyse <https://github.com/wdecoster/nanolyse>`__: Streaming script
        for filtering a fastq file to remove reads mapping to the lambda phage
        genome (control DNA used in nanopore sequencing). Uses
        `minimap2/mappy <https://github.com/lh3/minimap2>`__.
        
        Modules
        ~~~~~~~
        
        `nanoget <https://github.com/wdecoster/nanoget>`__: Functions for
        extracting features from reads, alignments and albacore summary data,
        parallelized.
        
        `nanomath <https://github.com/wdecoster/nanomath>`__: Functions for
        mathematical processing and calculating statistics.
        
        Test data
        ~~~~~~~~~
        
        `nanotest <https://github.com/wdecoster/nanotest>`__ provides small test
        datasets in fastq, bam and summary format (not included when installing
        NanoPack)
        
        ## CITATION If you use this tool, please consider citing our
        `publication <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
        
Keywords: nanopore sequencing processing analysis
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
