This GUI tool identifies which bacteria/virus, plasmids, and antibiotic resistance genes are contained in your NGS DNA sequences. It supports short reads such as Illumina, low accuracy long reads like Nanopore, and long reads such as PacBio or pre-assembled reads It uses Mash Screen to identify the pathogens and plasmids. And KMA to identify which antibiotic resistance genes. The overall goal is to use Kmer based alignment to quickly perform the above steps in less than 5-10 minutes per sample. It is also expected to be more robust than assembly based methods.

1. Clone Repository
2. Install Conda if not already in environment
3. Create conda environment
4. Download Mash libraries.

1. Activate conda environment - conda activate KPIP
2. Run the GUI - ~/KPIP/KPIP_GUI.py

sudo apt update
sudo apt install git

git clone https://github.com/jiangweiyao/KPIP.git

Detailed instruction on the the Miniconda website for installing and configuring Miniconda: https://conda.io/projects/conda/en/latest/user-guide/install/linux.html

You can run the prepackaged script install_miniconda.sh in the repository to install into your home directory (recommended) by using the following command assuming SanitizeMe is downloaded into your home directory:

. ~/KPIP/install_miniconda.sh

We use conda to create an environment (that we can activate and deactivate) to install our dependent software and resolve their dependencies. This environment is called "KPIP".

conda create -n KPIP python=3 gooey tabulate pandas mash kma -y

The command to generate the environment is in the included conda_env.txt file.

The Mash databases are too big to include with KPIP. The included get_msh_db.sh file can automatically download the databases for you and put them in the default location for KPIP (~/KPIP/db/). You can also make and use your own databases following the instructions from Mash. You can run this with the following command:

sh get_msh_db.sh

Two KMA databases are included with KPIP - built from ResFinder or CARD. You can also use and make your own custom database per instructions from KMA.

There are significant differences between the purpose of the ResFinder and the CARD database. The CARD database attempts to contain all known genes that confer antibiotic resistance, even genes that are naturally prevalent in a bacteria. The ResFinder database attempts to contain only AR genes not naturally found in a bacteria. For example, Escherichia coli naturally contain a numer of efflux genes, which is why it is naturally resistant to many antibiotics. These efflux genes will be detected using the CARD database, but ignored using the ResFinder database. Plasmid contained AR genes such β-Lactamase Genes would be detected using both databases. In other words, the CARD database is intended to be comprehensive, while the ResFinder database is intended to be medically actionable.

Activating your environment makes the software you installed in that environment available for use. You will see "(KPIP)" in front bash after activation.

conda activate KPIP

Run the code (change path if it is installed else where.)

~/KPIP/KPIP_GUI.py

When you are finished running the workflow, exit out of your environment by running conda deactivate. Deactivating your environment exits out of your current environment and protects it from being modified by other programs. You can build as many environments as you want and enter and exit out of them. Each environment is separate from each other to prevent version or dependency clashes. The author recommands using Conda/Bioconda to manage your dependencies.

• Jiangwei Yao

Apache License 2.0