This directory contains the Oct. 2012 (Nleu_3.0/nomLeu3) assembly of the
    gibbon genome (nomLeu3, Gibbon Genome Sequencing Consortium ),
    as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:
    http://www.ncbi.nlm.nih.gov/genome/480
    http://www.ncbi.nlm.nih.gov/genome/assembly/506498
    http://www.ncbi.nlm.nih.gov/bioproject/13975

Files included in this directory:

nomLeu3.2bit - contains the complete gibbon/nomLeu3 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

nomLeu3.agp.gz - Description of how the assembly was generated from
    fragments.

nomLeu3.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.

nomLeu3.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

nomLeu3.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    January 10 2013 (open-4-0-0) version of RepeatMasker
    RepBase library: RELEASE 20120418

nomLeu3.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.

md5sum.txt - checksums of files in this directory

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.

nomLeu3.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

nomLeu3.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
nomLeu3.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
nomLeu3.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

nomLeu3.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/nomLeu3/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/nomLeu3/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu3/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

-----------------------------------------------------------------------------
GenBank Data Usage

The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
-----------------------------------------------------------------------------
      Name                          Last modified      Size  Description
Parent Directory - genes/ 2020-10-02 13:38 - md5sum.txt 2019-01-17 15:56 479 nomLeu3.2bit 2013-03-04 12:14 737M nomLeu3.agp.gz 2013-03-08 11:56 4.8M nomLeu3.chrom.sizes 2013-02-27 13:30 428K nomLeu3.chromAlias.txt 2020-09-29 10:49 822K nomLeu3.fa.gz 2013-03-08 12:10 855M nomLeu3.fa.masked.gz 2013-03-08 12:18 451M nomLeu3.fa.out.gz 2013-03-08 11:57 154M nomLeu3.gc5Base.wib 2019-01-17 14:51 540M nomLeu3.gc5Base.wig.gz 2019-01-17 14:51 12M nomLeu3.gc5Base.wigVarStep.gz 2013-02-27 16:16 1.4G nomLeu3.trf.bed.gz 2013-03-08 11:57 6.5M xenoMrna.fa.gz 2019-10-16 12:14 6.8G xenoMrna.fa.gz.md5 2019-10-16 12:14 49 xenoRefMrna.fa.gz 2019-10-16 12:15 331M xenoRefMrna.fa.gz.md5 2019-10-16 12:15 52