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UFCG

Description

ufcg website

UFCG pipeline provides methods for a genome-width taxonomic profiling and annotation of your own biological sequences of Fungi.

Environment Modules

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

Environment Variables

  • HPC_UFCG_DIR - installation directory
  • HPC_UFCG_BIN - executable directory

Additional Usage Information

Specification of a temporary working directory (-w) is mandatory when using ufcg profile (e.g.): 

$ ufcg profile -i <INPUT> -o <OUTPUT> -w <WORKING> [OPTIONS]

Note

You may also use ${SLURM_TMPDIR} for your working directory. UFCG will delete the temporary files after processing each input file.

Citation

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

Dongwook Kim, Cameron L M Gilchrist, Jongsik Chun, Martin Steinegger, UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D777–D784, https://doi.org/10.1093/nar/gkac894

Categories

biology, genomics