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WindowMasker is a denovo repeat finder from the NCBI, published in 2006[1].

UCSC Installation

It was taken from the NCBI C++ Toolkit (Dec. 2005) and installed into


the following way:

ssh kolossus
cd /scratch/andy
tar xfz ncbi_cxx--Dec_31_2005.tar.gz 
cd ncbi_cxx--Dec_31_2005
./configure --without-debug --with-optimization --with-projects=src/app/winmasker/windowmasker.lst
cd /scratch/andy/ncbi_cxx--Dec_31_2005/GCC344-Release64/build && make all_p
cd app/winmasker/
cp windowmasker /cluster/bin/x86_64/

The README file in src/app/winmasker looks enough like a man file so

cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker
cp README /cluster/bin/man/man1/winmasker.1

Opossum Experiment

  • Running chr8 on hgwdev64 took about 5 min. Not bad.
  • Trying this thing genome-wide was a problem. It was never using more than 2 gigs of RAM and after about 2.5 hours it errored.
  • Running on the pitakluster was a problem too. Apparently this program communicates with the NCBI over the internet. Seems a little suspicious.
  • The results of the one-chromosome-at-a-time run on kolossus:
real    228m34.868s
user    72m38.388s
sys     15m1.872s


  1. Morgulis A, Gertz EM, Schaffer AA, Agarwala R. WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15. PubMed