Difference between revisions of "UFCG"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:BiologyCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ufcg}} |{{#vardefine:url|https://ufcg.steineggerlab.com}} <!-...") |
m |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 18: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | UFCG pipeline provides methods for a genome-width taxonomic profiling and annotation of your own biological sequences of Fungi. | + | 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 | ||
<!--Modules--> | <!--Modules--> | ||
| Line 25: | Line 32: | ||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 32: | Line 40: | ||
{{#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.): | |
| + | |||
| + | $ 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. | ||
|}} | |}} | ||
| Line 58: | Line 71: | ||
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]. | |
|}} | |}} | ||
Latest revision as of 17:41, 20 September 2023
Description
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: