Getting started

MetaSBT is a Python3 framework built for the analysis and characterization of the microbial dark matter. It is available on the Python Package Index as well as Conda on the Bioconda channel and relies on a set of external software dependencies described on the following sections.

Installing MetaSBT

The pipeline is available as a Python3 package that can be install with the following command:

pip install metasbt

It is also available as a conda package:

conda install -c bioconda metasbt

You may need to add the bioconda channel first by running:

conda config --add channels bioconda

The MetaSBT pipeline is also available by simply cloning this repository and installing the software with the following commands:

# Clone the MetaSBT repository
mkdir -p ~/git && cd ~/git
git clone https://github.com/cumbof/MetaSBT.git

# Move to the MetaSBT root folder
cd MetaSBT

# Finally install MetaSBT
make install

Once everything is installed, MetaSBT will be available on your environment. You can check whether it has been correctly installed by typing the following command in your terminal:

metasbt --version

You can check whether all the dependencies listed above are available on your system by running the following command:

metasbt --resolve-dependencies

You can also access the complete list of available arguments by specifying the --help option:

metasbt --help

Note: the same option is also available for all the MetaSBT modules (e.g.: metasbt profile --help will print the list of arguments available for the profile module).

The list of available modules is available by typing:

metasbt --modules

Dependencies

Please note that cloning this repository requires Git to be installed on your system.

In this last case, remember to check that the following external software dependencies are installed and available on your system:

• checkm (version >=1.2.0)
• howdesbt (version >=2.00.13)
• kitsune (version >=1.3.3)
• ncbitax2lin (version >=2.3.2)
• ntcard (version >=1.2.2)
• pip (version >=21.2.4)
• python (version >=3.7)
• wget (version >=1.21.3)

Note: MetaSBT makes use of some advanced howdesbt sub-commands that are not available by default when installing HowDeSBT. They must be enabled by compiling the software with the alternative version of the Makefile available in the root folder of the HowDeSBT repository on GitHub.

For what concerns CheckM, we strongly suggest to install it through pip or conda, but it will require in any case a couple of extra steps to correctly link the software to its database. This must be necessarily executed manually as reported on the official CheckM Wiki.

First, you need to download the last available database from the following repository https://data.ace.uq.edu.au/public/CheckM_databases/, decompress it on a dedicated location, and finally inform CheckM about where its database is located by typing:

checkm data setRoot <checkm_data_dir>

Note: MetaSBT is available for Linux and macOS only.