suvtk documentation

This is the documentation for the Submission of Uncultivated Viral genomes toolkit or suvtk (/ɛs juː viː tiː keɪ/).

Installation

  1. To install the package, run one of the following commands depending on your preferred package manager. The package is available on Bioconda and PyPI, so you can use either conda or mamba for installation. You can also install it using pip or from the source code for development purposes.:

conda create -n suvtk -c bioconda -c conda-forge suvtk
conda activate suvtk
suvtk --help

mamba create -n suvtk -c bioconda -c conda-forge suvtk
mamba activate suvtk
suvtk --help

pip install suvtk
suvtk --help

Warning

The pip installation does not include non-python dependencies like MMseqs2 and table2asn. You will need to install them separately.

git clone https://github.com/LanderDC/suvtk.git
cd suvtk
mamba create -n suvtk -c bioconda -c conda-forge 'python>=3.9' pip mmseqs2 table2asn
mamba activate suvtk
pip install .

  1. Download the database with:

suvtk download-database

Or manually download and extract it from Zenodo.

Background

The idea behind this package is to provide a toolkit to more easily submit viral sequences to Genbank. The package is designed to be user-friendly and provide a simpler experience by combining multiple resources. For example, suvtk follows MIUVIG and ICTV guidelines for the submission of uncultivated viral genomes and provides the suvtk table2asn subcommand as a wrapper around NCBI’s table2asn that only uses the necessary functionality for UViG submissions.

suvtk workflow diagram suvtk workflow diagram

Submission

Once you have your .sqn file generated by suvtk table2asn, you can submit it to Genbank by mailing it to gb-sub@ncbi.nlm.nih.gov.

Acknowledgements

A big thank you to: