This track depicts masked sequence as determined by WindowMasker on the the 08 Jan 2024 Pongo pygmaeus/GCF_028885625.2_NHGRI_mPonPyg2-v2.0_pri/GCF_028885625.2 genome assembly. The WindowMasker tool is included in the NCBI C++ toolkit. The source code for the entire toolkit is available from the NCBI FTP site.
To create this track, WindowMasker was run with the following parameters:
windowmasker -mk_counts true -input GCF_028885625.2_NHGRI_mPonPyg2-v2.0_pri.unmasked.fa -output wm_counts windowmasker -ustat wm_counts -sdust true -input GCF_028885625.2_NHGRI_mPonPyg2-v2.0_pri.unmasked.fa -output windowmasker.intervals perl -wpe 'if (s/^>lcl\|(.*)\n$//) { $chr = $1; } \ if (/^(\d+) - (\d+)/) { \ $s=$1; $e=$2+1; s/(\d+) - (\d+)/$chr\t$s\t$e/; }' windowmasker.intervals > windowmasker.sdust.bedThe windowmasker.sdust.bed included masking for areas of the assembly that are gap. The file was 'cleaned' to remove those areas of masking in gaps, leaving only the sequence masking. The final result covers 1,358,029,111 bases in the assembly size 3,220,951,552 for a percent coverage of % 42.16.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. PMID: 16287941