Difference between revisions of "EggNOG-mapper"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|eggnog-mapper}} |{{#vardefine:url|https://github.com/eggnogdb/eggnog-mapper}...") |
Johnbullard (talk | contribs) m (Added env variable for default database location) |
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|{{#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--> | ||
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
+ | * EGGNOG_DATA_DIR - application databases directory | ||
<!--Configuration--> | <!--Configuration--> | ||
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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. | + | Please cite the following two papers if you use eggNOG-mapper v2: |
+ | |||
+ | [1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain | ||
+ | prediction at the metagenomic scale. Carlos P. Cantalapiedra, | ||
+ | Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. | ||
+ | biorxiv (2021). doi: https://doi.org/10.1101/2021.06.03.446934 | ||
+ | [2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated | ||
+ | orthology resource based on 5090 organisms and 2502 viruses. Jaime | ||
+ | Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia | ||
+ | K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars | ||
+ | J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; | ||
+ | 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085 | ||
|}} | |}} |
Latest revision as of 19:29, 6 December 2021
Description
eggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only.
Environment Modules
Run module spider eggnog-mapper
to find out what environment modules are available for this application.
System Variables
- HPC_EGGNOG-MAPPER_DIR - installation directory
- HPC_EGGNOG-MAPPER_BIN - executable directory
- EGGNOG_DATA_DIR - application databases directory
Citation
If you publish research that uses eggnog-mapper you have to cite it as follows:
Please cite the following two papers if you use eggNOG-mapper v2: [1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. biorxiv (2021). doi: https://doi.org/10.1101/2021.06.03.446934 [2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085