This directory contains the Dec. 2008 assembly of the zebrafish genome
(danRer6, Wellcome Trust Sanger Institute, Zv8 assembly (CAAK00000000.5)), as well as repeat annotations and GenBank sequences.
This assembly was produced by The Wellcome Trust Sanger Institute in Cambridge, UK.
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
Files included in this directory:
- chr*.fa.gz: gzip compressed FASTA sequence of each chromosome.
Repeats (from RepeatMasker and Tandem Repeat Finder)
are in lower case while non-repeating sequence is in upper case.
- unmappedScaffolds.fa.gz: gzip compressed FASTA sequence of all the
unmapped scaffolds. These are repeatmasked as described above.
- md5sum.txt - Checksum file.
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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
[username: anonymous, password: your email address], then cd to the
directory goldenPath/danRer6/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/danRer6/chromosomes/ .
For a single file, e.g. chromFa.tar.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/chr1.fa.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/chr1.fa.gz'
-O chr1.fa.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 -
chr7.fa.gz 2010-01-25 16:07 24M
chr5.fa.gz 2010-01-25 16:07 23M
chr4.fa.gz 2010-01-25 16:08 21M
chr6.fa.gz 2010-01-25 16:08 19M
chr3.fa.gz 2010-01-25 16:08 19M
chr1.fa.gz 2010-01-25 16:09 18M
chr2.fa.gz 2010-01-25 16:09 18M
chr8.fa.gz 2010-01-25 16:09 17M
chr9.fa.gz 2010-01-25 16:10 17M
chr14.fa.gz 2010-01-25 16:10 16M
chr16.fa.gz 2010-01-25 16:10 16M
chr20.fa.gz 2010-01-25 16:10 16M
chr13.fa.gz 2010-01-25 16:11 16M
chr17.fa.gz 2010-01-25 16:11 15M
chr18.fa.gz 2010-01-25 16:11 15M
chr19.fa.gz 2010-01-25 16:11 15M
chr21.fa.gz 2010-01-25 16:12 15M
chr15.fa.gz 2010-01-25 16:12 15M
chr12.fa.gz 2010-01-25 16:12 14M
chr23.fa.gz 2010-01-25 16:12 14M
chr11.fa.gz 2010-01-25 16:12 14M
chr10.fa.gz 2010-01-25 16:13 13M
chr22.fa.gz 2010-01-25 16:13 13M
chr24.fa.gz 2010-01-25 16:13 12M
chr25.fa.gz 2010-01-25 16:13 12M
chrM.fa.gz 2010-01-25 16:13 5.4K
unmappedScaffolds.fa.gz 2010-01-25 16:25 56M
md5sum.txt 2010-01-26 15:30 1.2K