Installing GraphBin-Tk

GraphBin-Tk is now available on bioconda and PyPI.

Using conda

You can install GraphBin-Tk using the bioconda distribution. You can download Anaconda or Miniconda which contains conda. You can also use mamba instead of conda.

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

# create conda environment
conda create -n gbintk

# activate conda environment
conda activate gbintk

# install gbintk
conda install -c bioconda gbintk

# check gbintk installation
gbintk --help

Using pip

You can install GraphBin-Tk using pip from the PyPI distribution.

# install gbintk
pip install gbintk

# check gbintk installation
gbintk --help

Dependencies and external software checklist

Please make sure that the following dependencies and external software are properly installed before running GraphBin-Tk.

• python>=3.9,<3.13
• cogent3
• igraph
• cairocffi
• pycairo
• networkx
• scipy
• numpy
• pandas
• tqdm
• click
• tabulate
• graphbin
• graphbin2>=1.3.3
• metacoag>=1.2.1
• fraggenescan
• hmmer

You will need one of the following assemblers to obtain the metagenome assemblies depending on your read data.

• spades
• megahit
• flye

Available subcommands

Run gbintk --help or gbintk -h to list the help message for GraphBin-Tk.

Usage: gbintk [OPTIONS] COMMAND [ARGS]...

  gbintk (GraphBin-Tk): Assembly graph-based metagenomic binning toolkit

Options:
  -v, --version  Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  graphbin   GraphBin: Refined Binning of Metagenomic Contigs using...
  graphbin2  GraphBin2: Refined and Overlapped Binning of Metagenomic...
  metacoag   MetaCoAG: Binning Metagenomic Contigs via Composition,...
  prepare    Format the initial binning result from an existing binning tool
  visualise  Visualise binning and refinement results
  evaluate   Evaluate the binning results given a ground truth