Difference between revisions of "UFCG"
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(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ufcg}} |{{#vardefine:url|https://ufcg.steineggerlab.com}} <!-...") |
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| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
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| − | UFCG pipeline provides methods for a genome-width taxonomic profiling and annotation of your own biological sequences of Fungi. | + | UFCG pipeline provides 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 | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Specification of a temporary working directory (-w) is mandatory when using '''ufcg profile''' (e.g.): | |
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| + | ufcg profile -i <INPUT> -o <OUTPUT> [OPTIONS] -w ${SLURM_TMPDIR} | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | [https://doi.org/10.1093/nar/gkac894 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]. | |
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Revision as of 17:50, 15 September 2023
Description
UFCG pipeline provides 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
Additional Information
Specification of a temporary working directory (-w) is mandatory when using ufcg profile (e.g.):
ufcg profile -i <INPUT> -o <OUTPUT> [OPTIONS] -w ${SLURM_TMPDIR}