This directory contains the assembly of the Drosophila willistoni genome
(droWil1, Feb. 2006), as well as repeat annotations.

Files included in this directory:

droWil1.2bit - contains the complete Drosophila willistoni/droWil1 genome
    sequence in the 2bit file format.  Repeats from RepeatMasker and Tandem
    Repeats Finder (with period of 12 or less) are shown in lower case;
    non-repeating sequence is shown in upper case.  The utility program,
    twoBitToFa (available from the kent src tree), can be used to extract .fa
    file(s) from this file.  A pre-compiled version of the command line tool
    can be found at:
        http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
    See also:
        http://genome.ucsc.edu/admin/git.html
  http://genome.ucsc.edu/admin/jk-install.html

droWil1.agp.gz - Description of how the assembly was generated from
    fragments.

droWil1.fa.gz - "Soft-masked" assembly sequence in one file.
    Repeats from RepeatMasker and Tandem Repeats Finder (with period
    of 12 or less) are shown in lower case; non-repeating sequence is
    shown in upper case.

droWil1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

droWil1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.

droWil1.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

md5sum.txt - checksums of files in this directory


droWil1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

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If you plan to download a large file or multiple files from this 
directory, we recommend that you use ftp rather than downloading the 
files via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then 
go to the directory goldenPath/droWil1/bigZips. To download multiple 
files, use the "mget" command:

    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory)