Sequence
--------

  wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit
  wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/centromeres.txt.gz 
  gunzip centromeres.txt
  cut -f 2-5 centromeres.txt centromeres.bed
  twoBitMask hg38.2bit centromeres.bed hg38-centromeresMasked.2bit
  twoBitToFa hg38-centromeresMasked.2bit tmp.fa
  maskOutFa tmp.fa hard dfamseq
  rm tmp.fa



Benchmark
---------

  Garlic-1.3 
    createFakeSequence.pl -v -m hg19 -s 3099000000 --useBED --dir . -k 4 -o benchmark --no_repeats -l 2.2

  split -n 5 benchmark
  cat xaa > tmp
  echo >> tmp
  echo ">artificial_sequence_2" >> tmp
  cat xab  >> tmp
  echo >> tmp
  echo ">artificial_sequence_3" >> tmp
  cat xac  >> tmp
  echo >> tmp
  echo ">artificial_sequence_4" >> tmp
  cat xad  >> tmp
  echo >> tmp
  echo ">artificial_sequence_5" >> tmp
  cat xae  >> tmp
  rm xaa xab xac xad xae
  mv tmp benchmark

Process Into Dfam
-----------------

  /home/roberthubley/dfam/branches/release_2.0/Scripts/update/make_dfamseq.pl -a hg38 /var/lib/XfamProduction/Dfam/dfamseq/hg38