Metadata-Version: 2.1
Name: NanoComp
Version: 0.21.0
Summary: Comparing runs of Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoComp
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description: # NanoComp
        
        
        Compare multiple runs of long read sequencing data and alignments
        
        [![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/nanocomp.svg?branch=master)](https://travis-ci.org/wdecoster/nanocomp)
        
        ### INSTALLATION
        `pip install NanoComp`  
        
        This script is written for Python3.
        
        ### USAGE
        ```
        NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]
                        [--raw] [--readtype {1D,2D,1D2}] [--barcoded]
                        [--split_runs TSV_FILE]
                        [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                        [-n names [names ...]] [--plot {violin,box}] [--title TITLE]
                        (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])
        
        General options:
          -h, --help            show the help and exit
          -v, --version         Print version and exit.
          -t, --threads THREADS
                                Set the allowed number of threads to be used by the script
          -o, --outdir OUTDIR   Specify directory in which output has to be created.
          -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
          --verbose             Write log messages also to terminal.
          --raw                 Store the extracted data in tab separated file.
        
        Options for filtering or transforming input prior to plotting:
          --readtype {1D,2D,1D2}
                                Which read type to extract information about from summary. Options are 1D, 2D,
                                1D2
          --barcoded            Barcoded experiment in summary format, splitting per barcode.
          --split_runs TSV_FILE
                                File: Split the summary on run IDs and use names in tsv file. Mandatory header
                                fields are 'NAME' and 'RUN_ID'.
        
        Options for customizing the plots created:
          -f, --format {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}
                                Specify the output format of the plots.
          -n, --names names     Specify the names to be used for the datasets
          -c, --colors colors   Specify the colors to be used for the datasets
          --plot {violin,box, false}
                                Which plot type to use: 'boxplot', 'violinplot' (default) or 'false' (no plots)
          --title TITLE         Add a title to all plots, requires quoting if using spaces
        
        Input data sources, one of these is required.:
          --fastq files [files ...]
                                Data is in (compressed) fastq format.
          --fasta files [files ...]
                                Data is in (compressed) fasta format.
          --summary files [files ...]
                                Data is in (compressed) summary files generated by albacore or guppy.
          --bam files [files ...]
                                Data is in sorted bam files.
        
        ```
        
        [Example file for --split_runs](https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv)
        
        
        
        
        
        
        ### EXAMPLES
        ```
        NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs
        NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
        ```
        
        
        ### EXAMPLE OUTPUT
        ![loglength example](https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png)
        ![box percentIdentity example](https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png)
        
        [See more examples](https://github.com/wdecoster/nanocomp/tree/master/examples)
        
        I welcome all suggestions, bug reports, feature requests and contributions. Please leave an [issue](https://github.com/wdecoster/nanocomp/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 plotting quality control
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
