apscale 1.0.5

Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

apscale

Advanced Piepline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding data

Introduction

Apscale is a metabarcoding pipeline that handles the most common tasks in in metabarcoding pipelines like paired-end merging, primer trimming, quality filtering, otu clustering and denoising. It uses a simple command line 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.

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

To update apscale run:

pip install --upgrade apscale

Further dependencies

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.

How to use

Create a new apscale project

Apscale is oranized in projects with the following structure:

C:\USERS\DOMINIK\DESKTOP\EXAMPLE_PROJECT
├───1_raw data
│   └───data
├───2_demultiplexing
│   └───data
├───3_PE_merging
│   └───data
├───4_primer_trimming
│   └───data
├───5_quality_filtering
│   └───data
├───6_dereplication_pooling
│   └───data
│       ├───dereplication
│       └───pooling
├───7_otu_clustering
│   └───data
└───8_denoising
    └───data

A new project can be initialized with the command:

apscale --create_project NAME

If you prefer to have your data all in one place you can paste the raw data into 1_raw_data/data. Demultiplexing won't be handled by Apscale because there are to many different tagging systems out there at the moment. If you are using inline barcodes you can take a look at https://github.com/DominikBuchner/demultiplexer. If you are already starting with demultiplexed data please paste them into 2_demultiplexing/data.

Configuring the settings

Associated with every project Apscale with generate an Excel sheet in the project folder called "Settings.xlsx". It is divided into a seperate sheet for every module and a 0_general_settings tab.