This directory contains the Feb. 2006 assembly of the stickleback genome
(gasAcu1, Broad Institute version 1.0), as well as repeat annotations and 
GenBank sequences.

This assembly was produced by the Broad Institute at MIT and Harvard.
For more information on the stickleback genome, see the project website:
  http://www.broad.mit.edu/tools/data/data-vert.html

Files included in this directory:

gasAcu1.2bit - contains the complete stickleback/gasAcu1 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

chromAgp.tar.gz - Description of how the assembly was generated from
    fragments, unpacking to one file per chromosome.

chromFa.tar.gz - The assembly sequence in one file per chromosome.
    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.

chromFaMasked.tar.gz - The assembly sequence in one file per chromosome.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

chromOut.tar.gz - RepeatMasker .out files (one file per chromosome).
    RepeatMasker was run with the -s (sensitive) setting.
    The March 20 2006 (open-3-1-5) version of RepeatMasker and library 
    release 20060315 were used.

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format (one file per chromosome).

gasAcu1.quals.fa.gz - quality scores in fasta file format

md5sum.txt - checksums of files in this directory


gasAcu1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

gasAcu1.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

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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/gasAcu1/bigZips. To download multiple 
files, use the "mget" command:

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

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The stickleback sequence is made freely available before scientific 
publication with the following understanding: 

1. The data may be freely downloaded, used in analyses, and repackaged in
databases. 
2. Users are free to use the data in scientific papers analyzing particular 
genes and regions if the providers of these data (The Broad Institute) are 
properly acknowledged. 
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification of
regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that is,
30 Mb or more). 
4. Any redistribution of the data should carry this notice.