UFCG

Description

ufcg website  

UFCG (Universal Fungal Core Genes) is a pipeline that provides databases and methods for a genome-width taxonomic profiling and annotation of your own biological sequences of Fungi. The application includes the following:

• ufcg profile extracts marker gene sequences from your own Fungal biological data, including genome sequences, transcriptome sequences, and proteome sequences.
• ufcg tree reconstructs the phylogenetic relationship of the set of marker gene profiles.
• ufcg train generates sequence model of your own fungal marker gene, even from a small set of seed sequences.
• ufcg align conducts multiple sequence alignment of the genes from the set of marker gene profiles.

For usage information and options, load the module and call the method you want to use (e.g.): $ ufcg profile -h

Environment Modules

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

System Variables

• HPC_UFCG_DIR - installation directory
• HPC_UFCG_BIN - executable directory

Additional 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:

Kim, D., Gilchrist, C.L.M., Chun, J. & Steinegger, M. (2023) UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research, 51(D1), D777-D784, doi:10.1093/nar/gkac894.