Metadata-Version: 1.1
Name: NanoLyse
Version: 0.4.0
Summary: Removing reads mapping to the lambda genome
Home-page: https://github.com/wdecoster/nanolyse
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: NanoLyse
        ========
        
        | Remove reads mapping to the lambda phage genome from a fastq file.
        | This script uses Heng Li's
          `minimap2 <https://github.com/lh3/minimap2>`__ and his
          `mappy <https://pypi.python.org/pypi/mappy>`__ Python binding.
        
        |Twitter URL| |Build Status| |Code Health| |install with bioconda|
        
        INSTALLATION
        ~~~~~~~~~~~~
        
        ``pip install NanoLyse``
        
        USAGE
        ~~~~~
        
        ::
        
            Reads fastq from stdin and writes to stdout.  
        
            NanoLyse [-h] [-v] [-r REFERENCE]
        
                                Remove reads mapping to the lambda genome.
                                Reads fastq from stdin and writes to stdout.
        
                                Example usage:
                                zcat reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz
        
        
            optional arguments:
              -h, --help            show this help message and exit
              -v, --version         Print version and exit.
              -r REFERENCE, --reference REFERENCE
                                    Specify a reference fasta file against which to filter.
        
        WARNING
        ~~~~~~~
        
        If (some of) the reads of your genome of interest are sufficiently
        similar to the lambda genome those reads will be lost.
        
        EXAMPLES
        ~~~~~~~~
        
        | ``gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz``
        | In combination with
          `NanoFilt <https://github.com/wdecoster/nanofilt>`__:
        | ``gunzip -c reads.fastq.gz | NanoLyse | NanoFilt -q 12 | gzip > filtered_reads_without_lambda.fastq.gz``
        | Using a different genome to filter on (rather than lambda phage):
        | ``gunzip -c reads.fastq.gz | NanoLyse --reference mygenome.fa.gz | gzip > reads_without_mygenome.fastq.gz``
        
        I welcome all suggestions, bug reports, feature requests and
        contributions. Please leave an
        `issue <https://github.com/wdecoster/nanolyse/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
        .. |Build Status| image:: https://travis-ci.org/wdecoster/nanolyse.svg?branch=master
           :target: https://travis-ci.org/wdecoster/nanolyse
        .. |Code Health| image:: https://landscape.io/github/wdecoster/nanolyse/master/landscape.svg?style=flat
           :target: https://landscape.io/github/wdecoster/nanolyse/master
        .. |install with bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
           :target: http://bioconda.github.io/recipes/nanolyse/README.html
        
Keywords: nanopore sequencing processing
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
