This directory contains the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly
of the pig genome (susScr2, SGSC Sscrofa9.2
(NCBI project 10718, GCA_000003025.2))
in one gzip-compressed FASTA file per chromosome.

This assembly was produced by the Swine Genome Sequencing Consortium
and Wellcome Trust Sange Institute.

For more information on the pig genome, see the project website:
http://piggenome.org/
http://www.sanger.ac.uk/resources/

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.

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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/susScr2/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/susScr2/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/chromosomes/chrM.fa.gz' 
        -O chrM.fa.gz
    
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

      Name                    Last modified      Size  Description
      Parent Directory                             -   
      md5sum.txt              2010-03-31 10:54  909   
      chrX.fa.gz              2010-03-31 10:24   39M  
      chrM.fa.gz              2010-03-31 10:25  5.4K  
      chr18.fa.gz             2010-03-31 10:25   17M  
      chr17.fa.gz             2010-03-31 10:25   20M  
      chr16.fa.gz             2010-03-31 10:25   24M  
      chr15.fa.gz             2010-03-31 10:24   42M  
      chr14.fa.gz             2010-03-31 10:23   46M  
      chr13.fa.gz             2010-03-31 10:23   45M  
      chr12.fa.gz             2010-03-31 10:25   18M  
      chr11.fa.gz             2010-03-31 10:25   25M  
      chr10.fa.gz             2010-03-31 10:25   21M  
      chr9.fa.gz              2010-03-31 10:24   41M  
      chr8.fa.gz              2010-03-31 10:25   37M  
      chr7.fa.gz              2010-03-31 10:24   42M  
      chr6.fa.gz              2010-03-31 10:24   38M  
      chr5.fa.gz              2010-03-31 10:25   31M  
      chr4.fa.gz              2010-03-31 10:24   42M  
      chr3.fa.gz              2010-03-31 10:24   38M  
      chr2.fa.gz              2010-03-31 10:23   43M  
      chr1.fa.gz              2010-03-31 10:23   92M