This directory contains the Feb. 2009 assembly of the human genome (hg19,
GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1))
in one gzip-compressed FASTA file per chromosome.

The Feb. 2009 human reference sequence (GRCh37) was produced by the
Genome Reference Consortium:
	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/

Note on chrM:
Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion
sequence (represented as "chrM" in the Genome Browser) has been replaced in
GenBank with the record NC_012920. We have not replaced the original sequence,
NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge
Reference Sequence (rCRS, http://mitomap.org/bin/view.pl/MITOMAP/HumanMitoSeq)
in the next human assembly release.

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: Jan 29 2009 (open-3-2-7) version of RepeatMasker and
    RELEASE 20090120 of library RepeatMaskerLib.embl

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See also: Wellcome Trust Sanger Institute MHC Haplotype Project
for additional information on the chr6 alternate haplotype assemblies:
	http://www.sanger.ac.uk/HGP/Chr6/MHC/

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/hg19/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/hg19/chromosomes/ .
For a single file, e.g. chrM.fa.gz
    rsync -avzP 
        rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrM.fa.gz .
    
Or with wget, all files:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/*'
With wget, a single file:
    wget --timestamping 
        'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/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.
      Name                        Last modified      Size  Description
Parent Directory - md5sum.txt 2009-03-20 09:49 4.9K chrY.fa.gz 2009-03-20 09:02 7.9M chrX.fa.gz 2009-03-20 09:00 47M chrUn_gl000249.fa.gz 2009-03-20 09:02 13K chrUn_gl000248.fa.gz 2009-03-20 09:02 13K chrUn_gl000247.fa.gz 2009-03-20 09:02 11K chrUn_gl000246.fa.gz 2009-03-20 09:02 13K chrUn_gl000245.fa.gz 2009-03-20 09:02 12K chrUn_gl000244.fa.gz 2009-03-20 09:02 13K chrUn_gl000243.fa.gz 2009-03-20 09:02 14K chrUn_gl000242.fa.gz 2009-03-20 09:02 14K chrUn_gl000241.fa.gz 2009-03-20 09:02 14K chrUn_gl000240.fa.gz 2009-03-20 09:02 13K chrUn_gl000239.fa.gz 2009-03-20 09:02 10K chrUn_gl000238.fa.gz 2009-03-20 09:02 13K chrUn_gl000237.fa.gz 2009-03-20 09:02 14K chrUn_gl000236.fa.gz 2009-03-20 09:02 14K chrUn_gl000235.fa.gz 2009-03-20 09:02 12K chrUn_gl000234.fa.gz 2009-03-20 09:02 14K chrUn_gl000233.fa.gz 2009-03-20 09:02 13K chrUn_gl000232.fa.gz 2009-03-20 09:02 14K chrUn_gl000231.fa.gz 2009-03-20 09:02 9.2K chrUn_gl000230.fa.gz 2009-03-20 09:02 13K chrUn_gl000229.fa.gz 2009-03-20 09:02 6.6K chrUn_gl000228.fa.gz 2009-03-20 09:02 33K chrUn_gl000227.fa.gz 2009-03-20 09:02 41K chrUn_gl000226.fa.gz 2009-03-20 09:02 1.9K chrUn_gl000225.fa.gz 2009-03-20 09:02 56K chrUn_gl000224.fa.gz 2009-03-20 09:02 49K chrUn_gl000223.fa.gz 2009-03-20 09:02 57K chrUn_gl000222.fa.gz 2009-03-20 09:02 60K chrUn_gl000221.fa.gz 2009-03-20 09:02 50K chrUn_gl000220.fa.gz 2009-03-20 09:02 51K chrUn_gl000219.fa.gz 2009-03-20 09:02 56K chrUn_gl000218.fa.gz 2009-03-20 09:02 52K chrUn_gl000217.fa.gz 2009-03-20 09:02 55K chrUn_gl000216.fa.gz 2009-03-20 09:02 42K chrUn_gl000215.fa.gz 2009-03-20 09:02 56K chrUn_gl000214.fa.gz 2009-03-20 09:02 41K chrUn_gl000213.fa.gz 2009-03-20 09:02 53K chrUn_gl000212.fa.gz 2009-03-20 09:02 60K chrUn_gl000211.fa.gz 2009-03-20 09:02 54K chrM.fa.gz 2009-03-20 09:02 5.4K chr22.fa.gz 2009-03-20 09:02 11M chr21_gl000210_random.fa.gz 2009-03-20 09:02 9.0K chr21.fa.gz 2009-03-20 09:02 11M chr20.fa.gz 2009-03-20 09:02 19M chr19_gl000209_random.fa.gz 2009-03-20 09:02 47K chr19_gl000208_random.fa.gz 2009-03-20 09:02 21K chr19.fa.gz 2009-03-20 09:02 17M chr18_gl000207_random.fa.gz 2009-03-20 09:02 1.4K chr18.fa.gz 2009-03-20 09:01 23M chr17_gl000206_random.fa.gz 2009-03-20 09:02 13K chr17_gl000205_random.fa.gz 2009-03-20 09:02 53K chr17_gl000204_random.fa.gz 2009-03-20 09:02 26K chr17_gl000203_random.fa.gz 2009-03-20 09:02 13K chr17_ctg5_hap1.fa.gz 2009-03-20 09:02 501K chr17.fa.gz 2009-03-20 09:01 24M chr16.fa.gz 2009-03-20 09:01 24M chr15.fa.gz 2009-03-20 09:01 26M chr14.fa.gz 2009-03-20 09:01 28M chr13.fa.gz 2009-03-20 09:01 30M chr12.fa.gz 2009-03-20 09:01 41M chr11_gl000202_random.fa.gz 2009-03-20 09:02 13K chr11.fa.gz 2009-03-20 09:00 41M chr10.fa.gz 2009-03-20 09:00 41M chr9_gl000201_random.fa.gz 2009-03-20 09:02 12K chr9_gl000200_random.fa.gz 2009-03-20 09:02 61K chr9_gl000199_random.fa.gz 2009-03-20 09:02 24K chr9_gl000198_random.fa.gz 2009-03-20 09:02 18K chr9.fa.gz 2009-03-20 09:00 38M chr8_gl000197_random.fa.gz 2009-03-20 09:02 12K chr8_gl000196_random.fa.gz 2009-03-20 09:02 13K chr8.fa.gz 2009-03-20 09:00 45M chr7_gl000195_random.fa.gz 2009-03-20 09:02 60K chr7.fa.gz 2009-03-20 08:59 48M chr6_ssto_hap7.fa.gz 2009-03-20 09:02 1.3M chr6_qbl_hap6.fa.gz 2009-03-20 09:02 1.3M chr6_mcf_hap5.fa.gz 2009-03-20 09:02 1.2M chr6_mann_hap4.fa.gz 2009-03-20 09:02 1.3M chr6_dbb_hap3.fa.gz 2009-03-20 09:02 1.3M chr6_cox_hap2.fa.gz 2009-03-20 09:02 1.5M chr6_apd_hap1.fa.gz 2009-03-20 09:02 768K chr6.fa.gz 2009-03-20 08:59 52M chr5.fa.gz 2009-03-20 08:59 56M chr4_gl000194_random.fa.gz 2009-03-20 09:02 61K chr4_gl000193_random.fa.gz 2009-03-20 09:02 57K chr4_ctg9_hap1.fa.gz 2009-03-20 09:02 190K chr4.fa.gz 2009-03-20 08:59 59M chr3.fa.gz 2009-03-20 08:58 61M chr2.fa.gz 2009-03-20 08:58 75M chr1_gl000192_random.fa.gz 2009-03-20 09:02 178K chr1_gl000191_random.fa.gz 2009-03-20 09:02 33K chr1.fa.gz 2009-03-20 08:58 70M