apscale-gui 1.0.11

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data - Graphical User Interface

APSCALE graphical user interface

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

- Apscale

- Apscale GUI

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.

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

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

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

Further dependencies - blastn

Apscale also calls blastn for the local blast modules. It should be installed and be in PATH to be executed from anywhere on the system.

Check the BLAST Software home page:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

you can download it from here:

https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

To check this, type:

blastn -version

and it should return the version number, for example:

blastn: 2.12.0+ Package: blast 2.12.0, build Jun 4 2021 04:06:33

Tutorial

Creating a new project

Create a new folder (e.g. on your desktop) and name it for example: 'APSCALE_projects'.

Now run the APSCALE GUI with:

python -m apscale_gui

You will be asked to select an output directory.

Select the folder you just created ('APSCALE_projects').

Now create a new project using the GUI by typing your desired name of the project (e.g. My_new_project'). A new folder in your output directory will be created.

Already existing project folders can be loaded from here in the future.

In this case a new, blank project folder was created.

The interace

When loading a project you will be greeted by the APSCALE home window.

From here a multitude of DNA metabarcoding related tools can be started.

Check out the Tutorial for a more detailed overview of the respective tools (COMING SOON).

Running apscale: All-in-One Analysis

The APSCALE pipeline can easily be started via the All-in-One window.

First, open the settings file (either from within the GUI or from the project folder). Then adjust all settings according to the data set.

To run apscale, simply select the steps to run, click on 'Run analysis' and sit back and enjoy!

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. Furthermore, the ESV and OTU tables are compatible with TaxonTableTools (https://github.com/TillMacher/TaxonTableTools), which can be used for DNA metabarcoding specific analyses.