This directory contains the Monodelphis domestica genome 
(UCSC monDom4, January 2006) from The Broad Institute.

Files included in this directory:

Monodelphis4.0.agp.gz - Description of how the assembly was generated from
     fragments.

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.  Repeat Masker database version: 20060120

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 file for chromosomes. These were 
    created by RepeatMasker at the -s sensitive setting.

chromTrf.tar.gz - Tandem Repeats Finder locations, filtered to keep 
    repeats with period of less than or equal to 12, and translated 
    into one .bed file per chromosome.  

monDom4.2bit - contains the complete monDom4 Opossum Genome
    in the 2bit format.  A utility program, twoBitToFa (available
    from our src tree), can be used to extract .fa file(s) from
    this file.  See also:
	http://genome.ucsc.edu/admin/cvs.html - CVS access to the source tree
	http://genome.ucsc.edu/admin/jk-install.html - building the utilities

monDom4.quals.fa.gz - quality scores in fasta file format

md5sum.txt - MD5 checksum of these files to verify correct transmission


monDom4.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 you use rsync, wget, or ftp rather than downloading the
files via our website. To do so, anonymous ftp to hgdownload.cse.ucsc.edu,
go to the directory goldenPath/monDom4/bigZips/.

To download multiple files via ftp, use the "mget" command:
mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 

The rsync command to download the entire directory:
    rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP \
     rsync://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping \
	'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/*'
With wget, a single file:
    wget --timestamping \
    'ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/chromFa.tar.gz' \
	-O chromFa.tar.gz

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

All the files in this directory are freely usable for any purpose. 

This file last updated: 2009-06-10 - 10 June 2009