NGS Toolkit

Download

Full Download - Please download the zip file of the latest release (on the right side under 'Release')
Partial Download - Download the zip file under 'Code' (this does not include the wsl distribution file)

Partial Download is only recommended if the wsl distribution file ('ngstoolkitdist.tar') is already downloaded. Download of this version is much faster.

Installation

Full Download

1. Extract the zip file
2. Execute the installation script - register_distribution.py
3. Open the GUI (gui.py)

Partial Download

1. Extract the zip file
2. Copy the wsl distribution file ('ngstoolkitdist.tar') to the directory
3. Execute the installation script - register_distribution.py
4. Open the GUI (gui.py)

Usage

The input files for the Tool are FASTQ files (zipped files are accepted). Additionally to the FASTQ file a mapping file can be provided (not mandatory). The mapping file needs to be in a certain format

Mapping File

Tab seperated text file
First column = #SampleID
Please avoid to use special characters (no spaces in header names are allowed)

Spike removal

If your data set include spike controls a mapping file is mandatory

Mapping File for Spike Removal

Tab seperated text file
First column = #SampleID
Mandatory column = total_weight_in_g
Mandatory column = total_amount
If the stool weight is unknwon please write NA
If the amount of added spike is unknown please write NA
Please avoid to use special characters (no spaces in header names are allowed)

HELP

For installation and useability a README file is provided and can be found in the downloaded folder.

Execute

Get program version

python3 -m ngspipeline.cli -v

Build WSL distribution tar file

python3 -m ngspipeline.cli --export

Speedup and custom files

64-bit USEARCH

If you have a binary for the 64-bit version of USEARCH, you may put this into the wsl_distro_build/build-context/opt folder. Notice that according to the licence, you are only allowed to run one instance of the binary at any time.

The free 32-bit version may be sufficient for small studies; this will be downloaded automatically in the build process and does not require you to put the binary in the opt folder.

pre-build SILVA-derived databases

You can put the SILVA-derived databases in the wsl_distro_build/build-context/opt folder, in order to simply copy them and skip the resource and time intensive build process.

For extracting these databases from a distribution tar file a helper script exists:

bash ./helper-scripts/extract-silva-databases-from-tar.sh ngstoolkitdist.tar wsl_distro_build/build-context/opt