RepeatModeler¶
RepeatModeler screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RepeatModeler is available to install from the Bioconda Anaconda channel.
Installation¶
Load the default Miniforge module:
module load miniforge
If required, create a new Conda environment:
mamba create -n rm_env
Activate your Conda environment:
mamba activate rm_env
In your activated environment, install RepeatModeler from the Bioconda Anaconda channel, additionally specifying the Conda Forge channel for any additional required dependencies:
mamba install -c bioconda -c conda-forge repeatmodeler
Usage¶
To run the installed version of RepeatModeler, simply load the miniforge module
and activate your Conda environment:
module load miniforge
mamba activate rm_env
For usage documentation, run RepeatModeler -help:
(rm_env) $ RepeatModeler -help
No database indicated
NAME
RepeatModeler - Model repetitive DNA
SYNOPSIS
RepeatModeler [-options] -database <XDF Database>
Example jobs¶
Core Usage
To ensure that RepeatModeler uses the correct number of cores, the
-threads ${NSLOTS} option must be used.
Serial jobs¶
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load miniforge
mamba activate rm_env
# create a database for RepeatModeler
BuildDatabase -name DB_NAME INPUT.fa
Here is an example job running on 4 cores and 4GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
module load miniforge
mamba activate rm_env
RepeatModeler -database DB_NAME -threads ${NSLOTS}