Metadata-Version: 1.2
Name: nanopack
Version: 1.0.2
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: MIT
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
