Metadata-Version: 1.1
Name: NanoFilt
Version: 1.1.2
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: Nanofilt
        ========
        
        Filtering and trimming of Oxford Nanopore sequencing data.
        
        | 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:
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
            pip install nanofilt
            pip install nanofilt --upgrade
        
        NanoFilt is written for Python 3, but should also work for python2.7.
        
        USAGE:
        ~~~~~~
        
        ::
        
            usage: 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
        
        Example:
        
        .. code:: bash
        
            zcat reads.fastq.gz | NanoFilt -q 10 -l 500 --headcrop 50 | bwa mem -t 48 -x ont2d genome.fa - | samtools sort -O BAM -@24 -o alignment.bam -
            zcat reads.fastq.gz | NanoFilt -q 12 --headcrop 75 | gzip > trimmed-reads.fastq.gz
            zcat reads.fastq.gz | NanoFilt -q 10 | gzip > highQuality-reads.fastq.gz
        
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
