geNomad¶

Description¶

geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatransciptomes.

Environment Modules¶

Run module spider genomad to find out what environment modules are available for this application.

Environment Variables¶

HPC_GENOMAD_DIR - installation directory
HPC_GENOMAD_BIN - executable directory
HPC_GENOAD_DOC - documents directory

Additional Usage Information¶

Requried database is installed for all users at /data/reference/genomad/.

Citation¶

If you publish research that uses genomad you have to cite it as follows:

You can move, but you can’t hide: identification of mobile genetic elements with geNomad Antonio Pedro Camargo, Simon Roux, Frederik Schulz, Michal Babinski, Yan Xu, Bin Hu, Patrick S. G. Chain, Stephen Nayfach, Nikos C. Kyrpides bioRxiv 2023.03.05.531206; doi: https://doi.org/10.1101/2023.03.05.531206

Categories¶

biology, genomics