dRep
dRep is a genome de-replication tool.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | dRep/3.6.2 |
| BGSC | N/A |
Note
You can simply use module load dRep to activate the most recently installed version of this software.
Info
Make sure to properly capitalize the name of this module!
Commands / Options
This is a list of commands for the dRep command that we wanted to highlight. See the documentation for more arguments/options.
| Option | Description |
|---|---|
| check_dependencies | Ensure that all dependencies are installed |
| compare | Compare/cluster genomes |
| dereplicate | De-replicate genomes |
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load dRep/3.6.2 # Load dRep
dRep check_dependencies # Ensure that all dRep dependencies
Real Example
Has your research group used dRep in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of dRep.
Matthew R. Olm, Christopher T. Brown, Brandon Brooks, Jillian F. Banfield bioRxiv 108142; doi: https://doi.org/10.1101/108142