Installation#

Create virtual environments to run noise2read.

1. Create a Virtual Environment#

  • using conda (recommended because I developed noise2read using conda environment)

conda create -n noise2read_env python=3.8

conda activate noise2read_env

Or

  • using python venv

mkdir noise2read

cd noise2read

python -m venv noise2read_env

source noise2read_env/bin/activate

Note

make sure you have installed and currently using python >=3.8

2. Install noise2read#

  • Install via bioconda

conda install -c bioconda noise2read

conda install py-xgboost-gpu

Note

Currently, noise2read at bioconda requires installing py-xgboost-gpu separately. I will include this dependency in later release.

  • Install via pip

    pip install noise2read

    • dependencies available at pip will be installed automatically

    • install dependencies only available at bioconda

      conda install -c bioconda seqtk bcool

  • source code clone and Installation

git clone https://github.com/Jappy0/noise2read.git

cd noise2read

pip install -e .

  • Optional to install pygraphviz if you need the visualised read graph.

conda install -c conda-forge pygraphviz