Use when masking repetitive or low-complexity regions in genomic sequences before alignment or database searches
windowmasker/home/vimalinx/miniforge3/envs/bio/bin/windowmaskerreferences/help.md# 1) Stage 1: build unit-count statistics from FASTA
windowmasker \
-mk_counts \
-in genome.fa \
-out genome.counts
# 2) Stage 2: apply those counts to produce interval masks
windowmasker \
-ustat genome.counts \
-in genome.fa \
-out genome.mask.interval \
-outfmt interval
# 3) Produce masked FASTA and combine with DUST
windowmasker \
-ustat genome.counts \
-in genome.fa \
-out genome.masked.fa \
-outfmt fasta \
-dust true
-mk_counts first on representative input to generate unit-count statistics.-ustat during the masking stage.-outfmt based on downstream expectations, keeping in mind the default is interval output.-mk_counts and masking-stage options are separate modes; many arguments are mutually exclusive across them.-convert is for converting count-file formats, not for performing the normal masking stage.interval, not FASTA.-mem applies to count generation, while -smem targets the size of the generated counts file.