This directory contains the May 2010 (Broad AnoCar2.0/anoCar2)
assembly of the lizard genome
(anoCar2, Broad Institute of MIT and Harvard AnoCar 2.0 (GCA_000090745.1)),
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 lizard genome, see the project website:
http://www.broad.mit.edu/models/anole/

WGS assembly information: http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AAWZ02

Files included in this directory:

anoCar2.2bit - contains the complete lizard/anoCar2 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

anoCar2.agp.gz - Description of how the assembly was generated from
    fragments.

anoCar2.fa.gz - "Soft-masked" assembly sequence in one file.
    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.

anoCar2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

anoCar2.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  RepeatMasker version: June 30 2010 (open-3-2-9) 

anoCar2.trf.bed.gz - Tandem Repeats Finder locations, filtered to keep repeats
    with period less than or equal to 12, and translated into UCSC's BED
    format.

est.fa.gz - Lizard ESTs in GenBank. This sequence data is updated once a
    week via automatic GenBank updates.

md5sum.txt - checksums of files in this directory

mrna.fa.gz - Lizard mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.

xenoMrna.fa.gz - GenBank mRNAs from species other than that of 
    the genome. This sequence data is updated once a week via automatic 
    GenBank updates.

anoCar2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

anoCar2.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
anoCar2.gc5Base.wig.gz - wiggle database table for the GC Percent track
                    - this is an older standard alternative to the current
                    - bigWig format of the track, sometimes usefull for analysis
anoCar2.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:  http://genome.ucsc.edu/goldenPath/help/wiggle.html
    and  http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

anoCar2.chromAlias.txt - sequence name alias file, one line
    for each sequence name.  First column is sequence name followed by
    tab separated alias names.

------------------------------------------------------------------
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/anoCar2/bigZips. 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/anoCar2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/anoCar2/bigZips/chromFa.tar.gz' 
        -O chromFa.tar.gz

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

The Lizard 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 provider of these data (The Broad Institute) is 
      properly acknowledged.
   3. The center producing the data reserves 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.