This directory contains the Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) assembly of the
    alpaca genome (vicPac2, Broad Institute),
    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/905
    http://www.ncbi.nlm.nih.gov/genome/assembly/557168
    http://www.ncbi.nlm.nih.gov/bioproject/30567

Files included in this directory:

vicPac2.2bit - contains the complete alpaca/vicPac2 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

vicPac2.agp.gz - Description of how the assembly was generated from
    fragments.

vicPac2.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.

vicPac2.fa.masked.gz - "Hard-masked" assembly sequence in one file.
    Repeats are masked by capital Ns; non-repeating sequence is shown in
    upper case.

vicPac2.fa.out.gz - RepeatMasker .out file.  RepeatMasker was run with the
    -s (sensitive) setting.
    June 20 2013 (open-4-0-3) version of RepeatMasker
    RepBase library: RELEASE 20130422

vicPac2.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 - Alpaca 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 - Alpaca mRNA from GenBank. This sequence data is updated
    once a week via automatic GenBank updates.


vicPac2.chrom.sizes - Two-column tab-separated text file containing assembly
    sequence names and sizes.

vicPac2.gc5Base.wigVarStep.gz - ascii data wiggle variable step values used
                           - to construct the GC Percent track
vicPac2.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
vicPac2.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

------------------------------------------------------------------
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/vicPac2/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/vicPac2/bigZips/ .
For a single file, e.g. chromFa.tar.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac2/bigZips/chromFa.tar.gz .

Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/vicPac2/bigZips/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/vicPac2/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 Alpaca 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. 1. The data may
      be freely downloaded, used in analyses, and repackaged in databases.

-----------------------------------------------------------------------------
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 - vicPac2.chrom.sizes 2013-06-09 17:12 4.5M vicPac2.gc5Base.wigVarStep.gz 2013-06-09 17:21 1.0G vicPac2.2bit 2013-06-10 09:19 549M vicPac2.agp.gz 2013-06-28 14:39 6.0M vicPac2.fa.out.gz 2013-06-28 14:39 99M vicPac2.trf.bed.gz 2013-06-28 14:39 2.9M vicPac2.fa.gz 2013-06-28 14:50 662M vicPac2.fa.masked.gz 2013-06-28 14:57 435M vicPac2.gc5Base.wib 2019-01-17 14:54 409M vicPac2.gc5Base.wig.gz 2019-01-17 14:54 13M md5sum.txt 2019-01-17 15:59 479 mrna.fa.gz 2019-10-16 17:10 48K mrna.fa.gz.md5 2019-10-16 17:10 45 est.fa.gz 2019-10-16 17:15 626K est.fa.gz.md5 2019-10-16 17:15 44 xenoRefMrna.fa.gz 2019-10-16 17:16 331M xenoRefMrna.fa.gz.md5 2019-10-16 17:16 52 refMrna.fa.gz 2019-10-16 17:16 13K refMrna.fa.gz.md5 2019-10-16 17:16 48 genes/ 2020-02-05 13:47 -