This directory contains the Jan. 2010 (GGSC Nleu1.0/nomLeu1) assembly of the gibbon genome
(nomLeu1, GGSC (NCBI project 13975, accession GCA_000146795.1)), as well as repeat annotations and GenBank sequences.

This assembly was produced by the National Center for Biotechnology Information (NCBI).
For more information on the gibbon genome, see the project website:
http://www.ncbi.nlm.nih.gov/bioproject/13975

Files included in this directory:

nomLeu1.2bit - contains the complete gibbon/nomLeu1 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

nomLeu1.agp.gz - Description of how the assembly was generated from
    fragments.

nomLeu1.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.

nomLeu1.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

nomLeu1.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.  April 26 2011 (open-3-3-0) version of RepeatMasker
    with RepeatMaskerLib.embl RELEASE 20110920

nomLeu1.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

mrna.fa.gz - Gibbon 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.

nomLeu1.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

nomLeu1.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
nomLeu1.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
nomLeu1.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

nomLeu1.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/nomLeu1/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/nomLeu1/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/nomLeu1/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



      Name                          Last modified      Size  Description
Parent Directory - genes/ 2020-02-05 13:47 - md5sum.txt 2019-01-17 15:56 479 mrna.fa.gz 2019-10-17 14:31 28K mrna.fa.gz.md5 2019-10-17 14:31 45 nomLeu1.2bit 2010-10-31 16:50 731M nomLeu1.agp.gz 2011-11-21 12:16 4.7M nomLeu1.chrom.sizes 2010-10-29 15:35 288K nomLeu1.chromAlias.txt 2020-09-29 10:49 429K nomLeu1.fa.gz 2011-11-21 12:31 855M nomLeu1.fa.masked.gz 2011-11-21 12:41 454M nomLeu1.fa.out.gz 2011-11-21 12:17 152M nomLeu1.gc5Base.wib 2019-01-17 14:51 540M nomLeu1.gc5Base.wig.gz 2019-01-17 14:51 12M nomLeu1.gc5Base.wigVarStep.gz 2010-10-29 15:42 1.4G nomLeu1.trf.bed.gz 2011-11-21 12:17 6.5M xenoMrna.fa.gz 2016-03-16 11:54 5.0G xenoMrna.fa.gz.md5 2016-03-16 11:54 49 xenoRefMrna.fa.gz 2019-10-17 14:31 331M xenoRefMrna.fa.gz.md5 2019-10-17 14:31 52