Metadata-Version: 2.1
Name: NanoLyse
Version: 1.1.4
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: GPLv3
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](https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster)](https://twitter.com/wouter_decoster)
        [![Build Status](https://travis-ci.org/wdecoster/nanolyse.svg?branch=master)](https://travis-ci.org/wdecoster/nanolyse)
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/nanolyse/README.html)
        
        
        ### 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.
        
        
        ## 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
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
Description-Content-Type: text/markdown
