vConTACT

vConTACT can be used to manipulate NGS data. Two variants exists: one for version 0.11.3 of vConTACT2, and another for version 3.0.5 of vConTACT3.

Usage example

The following command loads the variant with vConTACT2, the vcontact2 command is made available:

module load vcontact release=2

The command below loads the default variant with vConTACT3, the vcontact3 command is made available:

module load vcontact

The vcontact_shell command can be used to access a shell in the bundles of all variants.

Run pet list -t vcontact for a list of examples.

Performance notes

No performance notes available

Recommended resources per session

vConTACT should be run on a system with at least 64 GB of RAM and 32 threads.

Benchmarks

No benchmarks available.

Community guides and tutorials

• No community guides available.

Official site and documentation

• vConTACT2
  • Site
  • Documentation
• vConTACT3
  • Site
  • Documentation

Licensing information

vConTACT2 is licensed under the GNU GPLv3 license, and vConTACT3 is licensed under the GNU GPLv3 license

Primary citation

For vConTACT2, use the following citation:

Bin Jang, H., Bolduc, B., Zablocki, O., Kuhn, J. H., Roux, S., Adriaenssens, E. M., … Sullivan, M. B. (2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology. doi

For vConTACT3, cite the following code repository

External guides and resources

• If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za