Metadata-Version: 1.2
Name: NanoFilt
Version: 1.9.2
Summary: Filtering and trimming of Oxford Nanopore Sequencing data
Home-page: https://github.com/wdecoster/nanofilt
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: Nanofilt
        ========
        
        Filtering and trimming of Oxford Nanopore sequencing data.
        
        \|Twitter URL\| \|conda badge\| \|Build Status\| \|Code Health\|
        
        | Filtering on quality and/or read length, and optional trimming after
          passing filters.
        | Reads from stdin, writes to stdout.
        
        | Intended to be used:
        | - directly after fastq extraction
        | - prior to mapping
        | - in a stream between extraction and mapping
        
        | See also
          ``my post about NanoFilt on my blog Gigabase or  gigabyte <https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/>`` \_\_.
        | Due to
          ``a  discrepancy <https://gigabaseorgigabyte.wordpress.com/2017/07/14/calculated-average-quality-vs-albacore-summary/>`` \_\_
          between calculated read quality and the quality as summarized by
          albacore this script takes since v1.1.0 optionally also a
          ``--summary`` argument. Using this argument with the
          sequencing\_summary.txt file from albacore will do the filtering using
          the quality scores from the summary. It's also faster.
        
        INSTALLATION AND UPGRADING:
        :sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``:sub:``~```````````\ ~\ :sub:``\ ~\`
        
        .. code:: bash
        
        ::
        
        ::
        
            pip install nanofilt
            pip install nanofilt --upgrade
        
        or
        
        \|conda badge\|
        
        .. code:: bash
        
        ::
        
        ::
        
            conda install -c bioconda nanofilt
        
        STATUS
        ------
        
        \|Build Status\| \|Code Health\|
        
        NanoFilt is written for Python 3.
        
        USAGE: :sub:``:sub:``\ :sub:`\`\` `
        
        ::
        
        ::
        
        ::
        
            NanoFilt [-h] [-q QUALITY] [-l LENGTH] [--headcrop HEADCROP] [--tailcrop TAILCROP]
        
            optional arguments:  
              -h, --help            show this help message and exit  
              -s --summary SUMMARYFILE optional, the sequencing_summary file from albacore for extracting quality scores
              -q, --quality QUALITY  Filter on a minimum average read quality score  
              -l, --length LENGTH Filter on a minimum read length  
              --headcrop HEADCROP   Trim n nucleotides from start of read  
              --tailcrop TAILCROP   Trim n nucleotides from end of read
              --minGC MINGC         Sequences must have GC content >= to this. Float
                                    between 0.0 and 1.0. Ignored if using summary file.
              --maxGC MAXGC         Sequences must have GC content <= to this. Float
                                    between 0.0 and 1.0. Ignored if using summary file.
        
        Example:
        
        .. code:: bash
        
        ::
        
        ::
        
            gunzip -c reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | minimap2 genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -
            gunzip -c reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz
            gunzip -c reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz
        
        .. \|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 .. \|conda badge\| image::
        https://anaconda.org/bioconda/nanofilt/badges/installer/conda.svg
        :target: https://anaconda.org/bioconda/nanofilt .. \|Build Status\|
        image:: https://travis-ci.org/wdecoster/nanofilt.svg?branch=master
        :target: https://travis-ci.org/wdecoster/nanofilt .. \|Code Health\|
        image::
        https://landscape.io/github/wdecoster/nanofilt/master/landscape.svg?style=flat
        :target: https://landscape.io/github/wdecoster/nanofilt/master
        
Keywords: nanopore sequencing processing trimming filtering
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
