Genome assembly soft-masking using Red (Repeat Detector)
Requires Red (REpeat Detector) software which you can get http://toolsmith.ens.utulsa.edu. Install one of the pre-built binaries for your system or build from source. The Red executable needs to be in your $PATH.
You can then run the Red mediated genome masking:
redmask.py -i genome.fa -o mygenome
This will run the masking generating the following files:
mygenome.softmasked.fa -- soft-masked genome
mygenome.repeats.bed -- BED file of repeats
mygenome.repeats.fasta -- FASTA file of masked sequences (putative repeats)