This directory contains the Jul. 2008 assembly of the zebra finch genome
(taeGut1, WUSTL v3.2.4) in one gzip-compressed FASTA file per chromosome.

This assembly was produced by the Genome Sequencing Center at the Washington 
University in St. Louis (WUSTL) School of Medicine. For more information on 
the zebra finch genome, see the project website:
    http://genome.wustl.edu/genome.cgi?GENOME=Taeniopygia%20guttata

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.
    Repeats from WindowMasker are shown in lower case; non-repeating sequence
    is shown in upper case.

  - Checksum values for all files in this directory can be found in
    md5sum.txt.

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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/taeGut1/chromosomes. To download multiple 
files, use the "mget" command:

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

Alternate methods to ftp access.
    
Using an rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/chromosomes/chrM.fa.gz' 
        -O chrM.fa.gz
    
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

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The Zebra finch sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
   if the providers of these data are properly acknowledged.  See
   http://genome.wustl.edu/data.cgi for credit information.

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.

4. This is in accordance with, and with the understandings in the Fort
   Lauderdale meeting discussing Community Resource Projects (see
   http://www.wellcome.ac.uk/doc_wtd003208.html) and the resulting
   NHGRI policy statement (http://www.genome.gov/page.cfm?pageID=10506537).

5. Any redistribution of the data should carry this notice.