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# Index fasta file
cd reference_July2020
bwa index dmerc.ctg.polished1.fa
#####################
# Run RepeatModeler 2.0.1
#####################
cd RepeatModeler-2.0.1
./BuildDatabase -name Dmerc_July2020 reference_July2020/dmerc.ctg.polished1.fa
singularity exec -B TandemRepeatFinder/trf:/opt/trf:ro docker://dfam/tetools:latest RepeatModeler -database Dmerc_July2020 -LTRStruct -pa 6
#####################
# Run RepeatMasker v4.0.9
#####################
# Hard-masked genome
singularity exec -B TandemRepeatFinder/trf:/opt/trf:ro docker://dfam/tetools:latest RepeatMasker -gccalc -s -nolow -norna -gff -pa 25 -lib RepeatModeler2/Dmerc_July2020-families.fa reference_July2020/dmerc.ctg.polished1.fa
# file name: dmerc.ctg.polished1.fa
# sequences: 330
# total length: 161570079 bp (161570079 bp excl N/X-runs)
# GC level: 40.33 %
# bases masked: 29808408 bp ( 18.45 %)
# Soft-masked genome
singularity exec -B TandemRepeatFinder/trf:/opt/trf:ro docker://dfam/tetools:latest RepeatMasker -xsmall -gccalc -s -nolow -norna -gff -pa 25 -dir repmasker_class_SOFTMASK -lib RepeatModeler2/Dmerc_July2020-families.fa reference_July2020/dmerc.ctg.polished1.fa