This directory contains the Dec. 2008 assembly of the zebrafish genome
(danRer6, Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)), as well as repeat annotations and GenBank sequences.

This assembly was produced by The Wellcome Trust Sanger Institute in Cambridge, UK.
For more information on the zebrafish genome, see the project website:

  http://www.sanger.ac.uk/Projects/D_rerio/

Files included in this directory:

  - chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
    Repeats (from RepeatMasker and Tandem Repeat Finder) 
    are in lower case while non-repeating sequence is in upper case.

  - unmappedScaffolds.fa.gz: gzip compressed FASTA sequence of all the 
    unmapped scaffolds. These are repeatmasked as described above.

  - md5sum.txt - Checksum file.

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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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/danRer6/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/danRer6/chromosomes/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/chr1.fa.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/chr1.fa.gz' 
        -O chr1.fa.gz

To unpack the *.tar.gz files:
    tar xvzf <file>.tar.gz
To uncompress the fa.gz files:
    gunzip <file>.fa.gz