This directory contains the Jun. 2011 (GGSC Nleu1.1/nomLeu2) assembly of the gibbon genome
(nomLeu2, Gibbon Genome Sequencing Consortium Nleu1.1 (NCBI project 13975, GCA_000146795.2, WGS ADFV01)), as well as repeat annotations and GenBank sequences.

For more information about this assembly, please note the NCBI resources:

Files included in this directory:

nomLeu2.2bit - contains the complete gibbon/nomLeu2 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:
    See also:

nomLeu2.agp.gz - Description of how the assembly was generated from

nomLeu2.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.

nomLeu2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

nomLeu2.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    April 26 2011 (open-3-3-0) version of RepeatMasker
    RepBase library: RELEASE 20110920

nomLeu2.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

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.

nomLeu2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

nomLeu2.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
nomLeu2.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
nomLeu2.gc5Base.wib    - binary data to correspond with the gc5Base.wig file
    see also:
         for a discussion of how to use the wig.gz and .wib files for
         interaction with the GC percent data values

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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/nomLeu2/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:// .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync:// .

Or with wget, all files:
    wget --timestamping 
With wget, a single file:
    wget --timestamping 
        -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 - md5sum.txt 2019-01-17 15:56 479 nomLeu2.2bit 2012-04-14 11:39 731M nomLeu2.agp.gz 2012-07-13 13:38 4.7M nomLeu2.chrom.sizes 2012-04-13 15:27 289K nomLeu2.fa.gz 2012-07-13 13:58 856M nomLeu2.fa.masked.gz 2012-07-13 14:08 449M nomLeu2.fa.out.gz 2012-07-13 13:41 154M nomLeu2.gc5Base.wib 2019-01-17 14:51 540M nomLeu2.gc5Base.wig.gz 2019-01-17 14:51 12M nomLeu2.gc5Base.wigVarStep.gz 2012-04-13 15:48 1.4G nomLeu2.trf.bed.gz 2012-07-13 13:41 6.5M xenoMrna.fa.gz 2016-03-16 11:10 5.0G xenoMrna.fa.gz.md5 2016-03-16 11:11 49 xenoRefMrna.fa.gz 2019-10-17 14:28 331M xenoRefMrna.fa.gz.md5 2019-10-17 14:28 52