DeePaC-strain

DeePaC-strain is a plugin for DeePaC (see below) shipping built-in models for predicting pathogenic potentials of novel strains of known bacterial species.

DeePaC

DeePaC is a python package and a CLI tool for predicting labels (e.g. pathogenic potentials) from short DNA sequences (e.g. Illumina reads) with interpretable reverse-complement neural networks. For details, see our preprint on bioRxiv: https://www.biorxiv.org/content/10.1101/535286v3 and the paper in Bioinformatics: https://doi.org/10.1093/bioinformatics/btz541. For details regarding the interpretability functionalities of DeePaC, see the preprint here: https://www.biorxiv.org/content/10.1101/2020.01.29.925354v2

Documentation can be found here: https://rki_bioinformatics.gitlab.io/DeePaC/.

Installation

We recommend using Bioconda (based on the conda package manager) or custom Docker images based on official Tensorflow images. Alternatively, a pip installation is possible as well.

With Bioconda (recommended)

You can install DeePaC with bioconda. Set up the bioconda channel first (channel ordering is important):

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

We recommend setting up an isolated conda environment:

# python 3.6, 3.7 and 3.8 are supported
conda create -n my_env python=3.8
conda activate my_env

and then:

# For GPU support (recommended)
conda install tensorflow-gpu deepacvir
# Basic installation (CPU-only)
conda install deepacvir

With Docker (also recommended)

Requirements:

• install Docker on your host machine.
• For GPU support, you have to install the NVIDIA Docker support as well.

See TF Docker installation guide and the NVIDIA Docker support installation guide for details. The guide below assumes you have Docker 19.03 or above.

You can then pull the desired image:

# Basic installation - CPU only
docker pull jbartoszewicz/deepac:0.13.5

# For GPU support
docker pull jbartoszewicz/deepac:0.13.5-gpu

And run it:

# Basic installation - CPU only
docker run -v $(pwd):/deepac -u $(id -u):$(id -g) --rm jbartoszewicz/deepac:0.13.5 deepac-strain --help
docker run -v $(pwd):/deepac -u $(id -u):$(id -g) --rm jbartoszewicz/deepac:0.13.5 deepac-strain test -q

# With GPU support
docker run -v $(pwd):/deepac -u $(id -u):$(id -g) --rm --gpus all jbartoszewicz/deepac:0.13.5-gpu deepac-strain test

# If you want to use the shell inside the container
docker run -it -v $(pwd):/deepac -u $(id -u):$(id -g) --rm --gpus all jbartoszewicz/deepac:0.13.5-gpu bash

The image ships the main deepac package along with the deepac-vir and deepac-strain plugins. See the basic usage guide below for more deepac commands. For more information about the usage of the NVIDIA container toolkit (e.g. selecting the GPUs to use), consult the User Guide.

With pip

We recommend setting up an isolated conda environment (see above). Alternatively, you can use a virtualenv virtual environment (note that deepac requires python 3):

# use -p to use the desired python interpreter (python 3.6 or higher required)
virtualenv -p /usr/bin/python3 my_env
source my_env/bin/activate

You can then install DeePaC with pip. For GPU support, you need to install CUDA and CuDNN manually first (see TensorFlow installation guide for details). Then you can do the same as above:

# For GPU support (recommended)
pip install tensorflow-gpu
pip install deepacvir

Alternatively, if you don’t need GPU support:

# Basic installation (CPU-only)
pip install deepacvir

Usage

DeePaC-strain may be used exactly as the base version of DeePaC. To use the plugin, substitute the deepac command for deepac-strain. Visit https://gitlab.com/rki_bioinformatics/DeePaC for a DeePaC readme describing basic usage.

For example, you can use the following commands:

# See help
deepac-strain --help

# Run quick tests (eg. on CPUs)
deepac-strain test -q
# Full tests
deepac-strain test -a

# Predict using a rapid CNN (trained on VHDB data)
deepac-strain predict -r input.fasta
# Predict using a sensitive LSTM (trained on VHDB data)
deepac-strain predict -s input.fasta

More examples are available at https://gitlab.com/rki_bioinformatics/DeePaC.

Supplementary data and scripts

In the main DeePaC repository (https://gitlab.com/rki_bioinformatics/DeePaC) you can find the R scripts and data files used in the papers for dataset preprocessing and benchmarking.

Cite us

If you find DeePaC useful, please cite:

@article{10.1093/bioinformatics/btz541,
    author = {Bartoszewicz, Jakub M and Seidel, Anja and Rentzsch, Robert and Renard, Bernhard Y},
    title = "{DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks}",
    journal = {Bioinformatics},
    year = {2019},
    month = {07},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz541},
    url = {https://doi.org/10.1093/bioinformatics/btz541},
    eprint = {http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz541/28971344/btz541.pdf},
}

@article {Bartoszewicz2020.01.29.925354,
    author = {Bartoszewicz, Jakub M. and Seidel, Anja and Renard, Bernhard Y.},
    title = {Interpretable detection of novel human viruses from genome sequencing data},
    elocation-id = {2020.01.29.925354},
    year = {2020},
    doi = {10.1101/2020.01.29.925354},
    publisher = {Cold Spring Harbor Laboratory},
    URL = {https://www.biorxiv.org/content/early/2020/02/01/2020.01.29.925354},
    eprint = {https://www.biorxiv.org/content/early/2020/02/01/2020.01.29.925354.full.pdf},
    journal = {bioRxiv}
}