run_dbcan¶
Description¶
This module loads the run_dbcan_new implementation of run_dbCAN, a standalone dbCAN3 annotation tool for automated CAZyme annotation in microbiomes. run_dbcan_new has multiple new features and improved pipeline performance.
- DBCAN_DB - dbcan reference directory * KRAKEN2_DB - kraken2 reference directory
Environment Modules¶
Run module spider run_dbcan
to find out what environment modules are available for this application.
Environment Variables¶
- HPC_RUN_DBCAN_DIR - installation directory
- HPC_RUN_DBCAN_BIN - executable directory
Additional Usage Information¶
Note: This installation also includes SignalP (version 4.1) peptide prediction. Use the flag --use_signalP=True
as in the following example to run SignalP with run_dbcan
:
run_dbcan EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655 --use_signalP=TRUE --db_dir $HPC_DBCAN_REF/db
Citation¶
If you publish research that uses run_dbcan you have to cite it as follows:
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin; dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101. http://doi.org/10.1093/nar/gky418
Categories¶
biology, genomics, annotation