Metadata-Version: 2.1
Name: apscale-gui
Version: 0.5
Summary: Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface
Home-page: https://github.com/TillMacher/apscale_gui
Author: Till-Hendrik Macher
Author-email: till-hendrik.macher@uni-due.de
License: MIT
Description: # APSCALE graphical user interface
        Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data
        
        ## Introduction
        The Apscale Graphical User Interface is a metabarcoding pipeline that handles the most common tasks in metabarcoding
        pipelines like paired-end merging, primer trimming, quality filtering, otu clustering and
        denoising. It uses a Graphical interface and is configured via a single configuration file.
        It automatically uses the available ressources on the machine it runs on while still providing the option
        to use less if desired.
        
        For more information on the pipeline running in the background visit [apscale](https://github.com/DominikBuchner/apscale)
        
        ## Installation
        
        Apscale can be installed on all common operating systems (Windows, Linux, MacOS).
        Apscale requires Python 3.7 or higher and can be easily installed via pip in any command line:
        
        `pip install apscale_gui`
        
        To update apscale_gui run:
        
        `pip install --upgrade apscale_gui`
        
        ### Further dependencies - vsearch
        
        Apscale calls vsearch for multiple modules. It should be installed and be in PATH to be executed
        from anywhere on the system.
        
        Check the vsearch Github page for further info:
        
        https://github.com/torognes/vsearch
        
        Support for compressed files with zlib is necessary. For Unix based systems this is shipped with
        vsearch, for Windows the zlib.dll can be downloaded via:
        
        [zlib for Windows](https://sourceforge.net/projects/mingw-w64/files/External%20binary%20packages%20%28Win64%20hosted%29/Binaries%20%2864-bit%29/zlib-1.2.5-bin-x64.zip/download)
        
        The dll has to be in the same folder as the vsearch executable. If you need help with adding a folder to PATH in windows
        please take a look at the first answer on this stackoverflow issue:
        
        [How to add a folder to PATH Windows](https://stackoverflow.com/questions/44272416/how-to-add-a-folder-to-path-environment-variable-in-windows-10-with-screensho)
        
        To check if everything is correctly set up please type this into your command line:
        
        `vsearch --version`
        
        It should return a message similar to this:
        
        ```
        vsearch v2.19.0_win_x86_64, 31.9GB RAM, 24 cores
        https://github.com/torognes/vsearch
        
        Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016)
        VSEARCH: a versatile open source tool for metagenomics
        PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584
        
        Compiled with support for gzip-compressed files, and the library is loaded.
        zlib version 1.2.5, compile flags 65
        Compiled with support for bzip2-compressed files, but the library was not found.
        ```
        
        ### Further dependencies - cutadapt
        
        Apscale also calls cutadapt with some modules. Cutadapt should be downloaded and installed
        automatically with the Apscale installation. To check this, type:
        
        `cutadapt --version`
        
        and it should return the version number, for example:
        
        `3.5`
        
        ## Tutorial
        ### Creating a new project
        ![](/_data/apscale_start.png "figure*1" =250x250)
        
        ### The interace
        ![](/_data/apscale_gui.png "figure*2" =250x250)
        
        ### Running apscale
        ![](/_data/apscale_run.png "figure*3" =250x250)
        
        ## Output
        
        Apscale will output an OTU table and an ESV table, as well as two .fasta files, which can be used for taxnomic assignment. For example, for COI sequences,
        BOLDigger (https://github.com/DominikBuchner/BOLDigger) can be used directly with the output of Apscale to assign taxomoy to the OTUs / ESVs using the Barcode of Life Data system (BOLD) database.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
