This directory contains the Dec. 2013 assembly of the human genome (hg38,
GRCh38 Genome Reference Consortium Human Reference 38 (GCA_000001405.15))
in one gzip-compressed FASTA file per chromosome.

The Dec. 2013 human reference sequence (GRCh38) was produced by the
Genome Reference Consortium:
	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Files included in this directory:

  - chr*.fa.gz: compressed FASTA sequence of each chromosome.

    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.

    RepeatMasker was run with the -s (sensitive) setting.
    Using: June 20 2013 (open-4-0-3) version of RepeatMasker and
    RepBase library: RELEASE 20130422 of library RepeatMaskerLib.embl

  - md5sum.txt - checksums of files in this directory

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The chr*_random sequences are unplaced sequence on those reference
chromosomes.

The chrUn_* sequences are unlocalized sequences where the corresponding
reference chromosome has not been determined.

See also: NCBI discussion of assembly procedures:
    http://www.ncbi.nlm.nih.gov/genome/assembly/assembly.shtml 

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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, then 
go to the directory goldenPath/hg38/chromosomes. 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/hg38/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chrM.fa.gz' 
        -O chrM.fa.gz
    
To uncompress the fa.gz files:
    gunzip <file>.fa.gz

All the files in this directory are freely available for public use.